Glutamine-rich maize seed protein and promoter

ABSTRACT

Provided is a nucleotide sequence encoding a 55 kDa maize prolamin family protein. Also provided is a nucleotide sequence derived from the promoter of the 55 kDa maize gene that can be used to express heterologous sequences in plants, and methods of using the disclosed nucleotide sequences.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Patent Application Ser. No. 60/551,286, filed Mar. 8, 2004, the disclosure of which is incorporated herein by reference in its entirety.

TECHNICAL FIELD

The presently disclosed subject matter relates generally to nucleic acids isolated from Zea mays. More particularly, the presently disclosed subject matter relates to nucleotide sequences encoding a member of the prolamin family of Zea mays cereal seed storage proteins, and to nucleotide sequences of a promoter of said prolamin family member. Also provided are methods of using the disclosed nucleic acid molecules in transgenic plants. Table of Abbreviations 2,4-D 2,4-dichlorophenoxyacetic acid AMV alfalfa mosaic virus β-ME β-mercaptoethanol BiP human immunoglobulin heavy-chain binding polypeptide bp basepair(s) CAB chlorophyll a/b binding CaMV cauliflower mosaic virus CDPK maize calcium-dependent protein kinase cM centimorgan(s) CMV cytomegalovirus DEAE diethyl aminoethyl DHFR dihydrofolate reductase DTT dithiothreitol EDTA ethylene diamine tetraacetic acid ELISA enzyme-linked immunosorbent assay EMCV encephalomyocarditis virus EPSP 5-enol-pyruvyl shikimate-3-phosphate ER endoplasmic reticulum EST expressed sequence tag GUS β-glucuronidase HEPES N-(2-hydroxyethyl)piperazine- N′-(2-ethanesulfonic acid) HSPs high scoring sequence pairs HSV-tk Herpes Simplex Virus thymidine kinase kb kilobase(s) k_(cat) catalytic constant kDa kilodalton(s) k_(m) Michaelis constant MCMV maize chlorotic mottle virus MDMV maize dwarf mosaic virus MTL metallothionein-like ORF open reading frame PAGE polyacrylamide gel electrophoresis PEG polyethylene glycol PEPC phosphoenol carboxylase pgk phosphoglycerate kinase Protox protoporphyrinogen oxidase psi pounds per square inch RFLPs restriction fragment length polymorphisms RUBISCO ribulose-1,5-bisphosphate carboxylase/oxygenase SDS sodium dodecyl sulfate SDS-PAGE sodium dodecyl sulfate polyacrylamide gel electrophoresis SSC standard saline citrate SSPE standard saline-phosphate-EDTA TEV tobacco etch virus T_(m) thermal melting point TMTD tetramethylthiuram disulfide TMV tobacco mosaic virus

Amino Acid Abbreviations, Codes, and Functionally Equivalent Codons Amino Acid 3-Letter 1-Letter Codons Alanine Ala A GCA; GCC; GCG; GCU Arginine Arg R AGA; AGG; CGA; CGC; CGG; CGU Asparagine Asn N AAC; AAU Aspartic; Acid Asp D GAC; GAU Cysteine Cys C UGC; UGU Glutamic; acid Glu E GAA; GAG Glutamine Gln Q CAA; CAG Glycine Gly G GGA; GGC; GGG; GGU Histidine His H CAC; CAU Isoleucine Ile I AUA; AUC; AUU Leucine Leu L UUA; UUG; CUA; CUC; CUG; CUU Lysine Lys K AAA; AAG Methionine; Met M AUG Phenylalanine Phe F UUC; UUU Proline Pro P CCA; CCC; CCG; CCU Serine Ser S ACG; AGU; UCA; UCC; UCG; UCU Threonine Thr T ACA; ACC; ACG; ACU Tryptophan Trp W UGG Tyrosine Tyr Y UAC; UAU Valine Val V GUA; GUC; GUG; GUU

BACKGROUND

An objective of crop trait functional genomics is to identify crop trait genes of interest, for example, genes capable of conferring useful agronomic traits in crop plants. Such agronomic traits include, but are not limited to, enhanced yield, whether in quantity or quality; enhanced nutrient acquisition and metabolic efficiency; enhanced or altered nutrient composition of plant tissues used for food, feed, fiber, or processing; enhanced utility for agricultural or industrial processing; enhanced resistance to plant diseases; enhanced tolerance of adverse environmental conditions including, but not limited to, drought, excessive cold, excessive heat, or excessive soil salinity or extreme acidity or alkalinity; and alterations in plant architecture or development, including changes in developmental timing. The deployment of such identified trait genes by either transgenic or non-transgenic approaches can materially improve crop plants for the benefit of agriculture.

Cereals are the most important crop plants on the planet in terms of both human and animal consumption. Genomic synteny (conservation of gene order within large chromosomal segments) is observed in rice, maize, wheat, barley, rye, oats, and other agriculturally important monocots including sorghum (see e.g., Kellogg, 1998; Song et al., 2001, and references therein), which facilitates the mapping and isolation of orthologous genes from diverse cereal species based on the sequence of a single cereal gene. Rice has the smallest (about 420 Mb) genome among the cereal grains, and has recently been a major focus of public and private genomic and EST sequencing efforts. See Goff et al., 2002.

The identification of genes that are important for crop development is an ongoing effort in the agricultural community. Additional information can also be derived from the analysis of the genomes of various important plants. For example, the identification of regulatory elements that control the expression of genes can also lead to the ability to manipulate the plant genome to express polypeptides of interest in specific tissues. In particular, certain plants are becoming the organisms of choice for large-scale production of commercially important proteins such as enzymes. This strategy takes advantage of the fact that during seed development, endosperm cells synthesize large amounts of storage proteins of the zein family, which are deposited in structures known as protein bodies derived from the endoplasmic reticulum. These protein bodies cofractionate with the gluten fraction produced in corn wet milling. The potential therefore exists to generate large quantities of recombinant enzymes in a form associated with gluten or in a more pure form following release of the recombinant enzyme activity from the gluten-associated or immobilized state.

What are needed, then, are new methods and reagents for expressing heterologous nucleotide sequences in plant cells. To meet these needs, the presently disclosed subject matter provides in some embodiments a promoter sequence for directing expression of heterologous nucleotide sequences in plant cells. Also provided are methods for expressing heterologous nucleotide sequences in plant cells using the disclosed promoter.

The presently disclosed subject matter addresses these problems associated with the expression of nucleotide sequences in transgenic plants, as well as other problems.

SUMMARY

This Summary lists several embodiments of the presently disclosed subject matter, and in many cases lists variations and permutations of these embodiments. This Summary is merely exemplary of the numerous and varied embodiments. Mention of one or more representative features of a given embodiment is likewise exemplary. Such an embodiment can typically exist with or without the feature(s) mentioned; likewise, those features can be applied to other embodiments of the presently disclosed subject matter, whether listed in this Summary or not. To avoid excessive repetition, this Summary does not list or suggest all possible combinations of such features.

The presently disclosed subject matter provides methods for expressing a nucleotide sequence in a plant. In some embodiments, the method comprises (a) operably linking the nucleotide sequence to a promoter comprising SEQ ID NO: 6 to produce an expression cassette; and (b) generating a transgenic plant comprising the expression cassette, whereby the nucleotide sequence is expressed in the plant. In some embodiments, the generating comprises transforming a plant cell with the expression cassette and regenerating the plant from the transformed plant cell. In some embodiments, the generating comprises homologously recombining the nucleotide sequence into an endogenous genetic locus under the control of a promoter comprising SEQ ID NO: 6. In some embodiments, the transforming is by biolistic transformation of a vector comprising the expression cassette. In some embodiments, the vector is a binary Agrobacterium expression vector.

In some embodiments, the nucleotide sequence encodes a polypeptide selected from the group consisting of carbohydrases, cellulases, hemicellulases, pectinases, isomerases, lyases, proteases, heat shock proteins, chaperonins, phytases, insecticidal proteins, antimicrobial proteins, a-amylases, glucoamylases, glucanases, glucosidases, xylanases, ferulic acid esterases, galactosidases, pectinases, and chymosin.

The presently disclosed subject matter also provides methods for expressing a nucleotide sequence in a plant. In some embodiments, the method comprises (a) operably linking the nucleotide sequence to a plant promoter, the nucleotide sequence comprising SEQ ID NO: 1 to produce an expression cassette; and (b) generating a transgenic plant comprising the expression cassette, whereby the nucleotide sequence is expressed in the plant. In some embodiments, the generating comprises transforming a plant cell with the expression cassette and regenerating the plant from the transformed plant cell. In some embodiments, the transforming is by biolistic transformation of a vector comprising the expression cassette. In some embodiments, the vector is a binary Agrobacterium expression vector.

The presently disclosed subject matter also provides methods for producing a heterologous polypeptide in a plant cell. In some embodiments, the method comprises (a) generating a plant cell comprising a nucleotide sequence encoding the heterologous polypeptide operably linked to SEQ ID NO: 6; and (b) expressing in the plant cell the nucleotide sequence encoding the heterologous polypeptide, whereby the heterologous polypeptide is produced in the plant cell. In some embodiments, the generating comprises transforming the plant cell with an expression cassette comprising the nucleotide sequence encoding the heterologous polypeptide. In some embodiments, the generating comprises homologously recombining the nucleotide sequence into an endogenous genetic locus under the control of a promoter comprising SEQ ID NO: 6 such that the nucleotide sequence becomes operably linked to SEQ ID NO: 6. In some embodiments, the transforming is by biolistic transformation of a vector comprising the expression cassette. In some embodiments, the vector is a binary Agrobacterium expression vector. In some embodiments, the instant method further comprises regenerating a plant from the plant cell. In some embodiments, the instant method further comprises isolating the polypeptide from the plant. In some embodiments, the polypeptide is located within a protein body of endoplasmic reticulum of the plant cell.

The methods and compositions of the presently disclosed subject matter can be used to produce a heterologous polypeptide of interest in a plant cell. In some embodiments, the nucleotide sequence encodes a polypeptide selected from the group consisting of carbohydrases, cellulases, hemicellulases, pectinases, isomerases, lyases, proteases, heat shock proteins, chaperonins, phytases, insecticidal proteins, antimicrobial proteins, a-amylases, glucoamylases, glucanases, glucosidases, xylanases, ferulic acid esterases, galactosidases, pectinases, and chymosin.

The presently disclosed subject matter also provides methods for targeting a protein of interest to a structure of a plant cell selected from the group consisting of endoplasmic reticulum (ER) and apoplast. In some embodiments, the method comprises (a) fusing a nucleic acid molecule encoding a signal sequence of a Zea mays Q protein in frame to a nucleotide sequence encoding the protein of interest, wherein the nucleic acid molecule encoding a signal sequence of a Zea mays Q protein and the nucleotide sequence encoding the protein of interest are operably linked to a promoter to produce a plant expression construct; and (b) transforming the plant cell with the plant expression construct, whereby the protein of interest is targeted to the structure.

The presently disclosed subject matter also provides methods for producing a plant seed with an increased nutritional value. In some embodiments, the method comprises (a) transforming a plant cell with an expression vector comprising a nucleotide sequence encoding SEQ ID NO: 2, or a fragment or derivative thereof; (b) regenerating a plant from the transformed plant cell; and (c) isolating a seed from the regenerated plant, whereby a seed with an increased nutritional value is produced. In some embodiments, the increased nutritional value is selected from the group consisting of an increased level of an essential amino acid, an improved amino acid balance, and an improved amino acid digestibility, when compared to a seed from a non-transformed plant of the same species.

The presently disclosed subject matter also provides methods for targeting a protein of interest to a protein body in a plant. In some embodiments, the method comprises (a) fusing a nucleic acid molecule encoding SEQ ID NO: 2, or a fragment or derivative thereof, in frame to a nucleotide sequence encoding the protein of interest, wherein the nucleic acid molecule encoding SEQ ID NO: 2, or the fragment or derivative thereof, and the nucleotide sequence encoding the protein of interest are operably linked to a promoter to produce a plant expression construct; and (b) transforming the plant cell with the plant expression construct, whereby the protein of interest is targeted to a protein body in the plant.

The presently disclosed subject matter also provides isolated nucleic acid molecules, expression cassettes, recombinant vectors, cells, and transgenic plants comprising the disclosed nucleic acid molecules and expression cassettes. In some embodiments, the nucleic acid molecules and expression cassettes comprise SEQ ID NO: 1, and in some embodiments the nucleic acid molecules and expression cassettes comprise SEQ ID NO: 6. In some embodiments, the expression cassette is expressed in seed and a polypeptide encoded by the expression cassette is located within a protein body of endoplasmic reticulum of a cell of the seed.

The methods and compositions of the presently disclosed subject matter can be used with any plant species. In some embodiments, the plant is a monocot. In some embodiments, the monocot is selected from the group consisting of rice, maize, wheat, barley, oats, rye, millet, sorghum, triticale, secale, einkorn, spelt, emmer, teff, milo, flax, gramma grass, Tripsacum, and teosinte. In some embodiments, the plant is selected from the group consisting of rice, wheat, barley, rye, maize, potato, canola, soybean, sunflower, carrot, sweet potato, sugarbeet, bean, pea, chicory, lettuce, cabbage, cauliflower, broccoli, turnip, radish, spinach, asparagus, onion, garlic, eggplant, pepper, celery, squash, pumpkin, cucumber, apple, pear, quince, melon, plum, cherry, peach, nectarine, apricot, strawberry, grape, raspberry, blackberry, pineapple, avocado, papaya, mango, banana, soybean, tobacco, tomato, sorghum and sugarcane. In some embodiments, the plant is maize.

In some embodiments of the presently disclosed subject matter, the expression cassette is expressed in a tissue selected from the group consisting of the epidermis, root, vascular tissue, meristem, cambium, cortex, pith, leaf, flower, seed, and combinations thereof. In some embodiments, the expression cassette is expressed in a seed and a polypeptide encoded by the nucleotide sequence is located within a protein body of endoplasmic reticulum of a cell of the seed.

Accordingly, it is an object of the presently disclosed subject matter to provide reagents and methods for expressing heterologous sequences in plant cells. This and other objects are achieved in whole or in part by the presently disclosed subject matter.

An object of the presently disclosed subject matter having been stated hereinabove, and which are addressed in whole or in part by the presently disclosed subject matter, other objects will become evident as the description proceeds when taken in connection with the accompanying drawings as best described hereinbelow.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts Western blot analysis of flour extracts using antisera to purified Nov9x phytase. The first lane on the blot depicts the positions of molecular weight standards (labeled on left). A188 is an extract of seed from non-transgenic corn. Nov9x phytase (predicted molecular weight 47 kDa) is identified as the prominent band migrating in the region of the 55 kDa standard. Nov9x phytase was not detected in the negative control (i.e. A188) corn flour extract.

FIG. 2 depicts SDS-PAGE analysis of proteins extracted from endosperm flour (endo.) or from embryo paste (embryo) from non-transgenic corn. Samples were run before (−) and after (+) heating the extract to 80° C. for 20 minutes.

FIG. 3 is a bar graph depicting the results of assaying α-galactosidase activity in flour from transgenic corn seeds that contain a fusion protein including the Q protein amino acid sequence fused to α-galactosidase. Activity is expressed as α-galactosidase units per gram of flour from individual seeds.

FIG. 4 is a bar graph depicting the results of assaying α-galactosidase activity in flour from transgenic corn seeds that contain a fusion protein including the Q protein signal sequence fused to α-galactosidase. Activity is expressed as α-galactosidase units per gram of flour from individual seeds.

BRIEF DESCRIPTION OF THE SEQUENCE LISTING

SEQ ID NO: 1 is a nucleotide sequence of the open reading frame of the Q protein gene.

SEQ ID NO: 2 is an amino acid sequence encoded by SEQ ID NO: 1.

SEQ ID NO: 3 is a nucleotide sequence from the Q protein cDNA that was employed in genomic walking experiments to identify the promoter of the Q protein gene (SEQ ID NO: 6).

SEQ ID NOs: 4 and 5 are the nucleotide sequences of two Q-protein-specific primers that were employed in the genomic walking experiments.

SEQ ID NO: 6 is the nucleotide sequence of a promoter from the Q protein gene that is capable of directing expression of operably linked nucleotide sequences.

SEQ ID NO: 7 is a partial N-terminal amino acid sequence of an abundant 27 kDa protein isolated from maize endosperm, which matches the amino-terminus of the 28 kDa maize glutelin-2 (γ-zein; GENBANK® Accession No. PO4706).

SEQ ID NO: 8 is a partial N-terminal amino acid sequence of the abundant 55 kDa protein isolated from maize endosperm.

SEQ ID NO: 9 is the amino acid sequence of the V5 epitope tag derived from the P and V proteins of the paramyxovirus of simian virus 5 (SV5).

SEQ ID NO: 10 is the amino acid sequence of a pentapeptide epitope tag.

SEQ IS NO: 11 is a C-terminal hexapeptide sequence present on recombinant Nov9x phytase.

SEQ ID NO: 12 is the amino acid sequence of the gene product of the phytase expression cassette.

SEQ ID NO: 13 is a nucleotide sequence of a Zea mays γ-zein promoter to which 5′ Hind III and a 3′ BamH I recognition sequences have been added.

SEQ ID NO: 14 is a nucleotide sequence of pNOV4061, an expression construct encoding a Nov9x phytase with a gamma zein signal sequence under the control of the gamma zein promoter.

SEQ ID NO: 15 is a nucleotide sequence of pNOV2117, an Agrobacterium binary vector encoding an E. coli manA phosphomannose isomerase polypeptide under the transcriptional control of a maize ubiquitin promoter.

SEQ ID NO: 16 is a nucleotide sequence of pNOV4325, an intermediate plasmid encoding a γ-zein-galA fusion protein separated by a 9 nucleotide linker.

SEQ ID NO: 17 is a nucleotide sequence of pNOV4349, an Agrobacterium binary vector based on pNOV2117 into which a Q-protein coding sequence has been inserted.

SEQ ID NO: 18 is a nucleotide sequence of pNOV4328, an intermediate plasmid encoding a γ-zein signal sequence/galA fusion protein under the transcriptional control of a γ-zein promoter.

DETAILED DESCRIPTION

The presently disclosed subject matter will be now be described more fully hereinafter with reference to the accompanying Examples, in which representative embodiments of the presently disclosed subject matter are shown. The presently disclosed subject matter can, however, be embodied in different forms and should not be construed as limited to the embodiments set forth herein. Rather, these embodiments are provided so that this disclosure will be thorough and complete, and will fully convey the scope of the presently disclosed subject matter to those skilled in the art.

All publications, patent applications, patents, and other references cited herein are incorporated by reference in their entireties.

I. General Considerations

A 55 kDa maize protein (designated Q protein) was identified, and appears to belong to the prolamin family of cereal seed storage proteins. The protein is released from endosperm flour in the presence of dithiothreitol (DTT) and is the second most abundant protein in these extracts after γ-zein, which by itself constitutes about 15% of endosperm protein. An expressed sequence tag (EST) sequence encoding a portion of the protein was retrieved from the GENBANK® database. Using oligonucleotide primers derived from the EST sequence, two overlapping cDNA clones were amplified. The combined clones encode a polypeptide chain of 308 residues including a predicted signal peptide of 19 residues. The deduced sequence of the mature protein is 289 amino acids and includes 104 Gln and 13 Glu. The combined percentage of Gln and Glu residues is 40%, more than twice that reported for other zeins. The predicted sequence also includes 5 Lys, an amino acid that is completely lacking in all other zeins except 6-zein, which has just one. The γ-zein protein accumulates on the periphery of protein bodies, and the co-fractionation of the 55 kDa Q protein and γ-zein suggests that both proteins accumulate in this region.

Previous efforts aimed at increasing Lys content of zeins for improved nutrition involved the insertion of 1-2 Lys residues into α-zein (Wallace et al., 1988) and up to 10 Lys residues into γ-zein (Torrent et al., 1987). The modified zeins accumulated in structures resembling protein bodies when synthesized in transient expression systems using either Xenopus oocytes or maize endosperm. However, both α-zein and γ-zein lack Lys and contain only 1-4 acidic amino acids that might otherwise serve to neutralize positively charge residues. By contrast, the deduced sequence of the 55 kDa Q protein contains a total of 16 acidic residues. The presence of 5 Lys in the 55 kDa protein and its apparent localization at or near the surface of protein bodies suggests that its native conformation can tolerate substitution of additional Lys residues.

II. Definitions

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the presently disclosed subject matter pertains. For clarity of the present specification, certain definitions are presented hereinbelow.

Following long-standing patent law convention, the terms “a”, “an”, and “the” refer to “one or more” when used in this application, including in the claims. Thus, the phrases “a cell” and “the cell” refer to one or more cells, unless the context is clearly to the contrary.

As used herein, the terms “associated with” and “operably linked” refer to two nucleotide sequences that are related physically or functionally. For example, a promoter or regulatory DNA sequence is said to be “associated with” a DNA sequence that encodes an RNA or a polypeptide if the two sequences are operably linked, or situated such that the regulator DNA sequence will affect the expression level of the coding or structural DNA sequence.

As used herein, the term “chimera” refers to a polypeptide that comprises domains or other features that are derived from different polypeptides or are in a position relative to each other that is not naturally occurring.

As used herein, the term “chimeric construct” refers to a recombinant nucleic acid molecule in which a promoter or regulatory nucleotide sequence is operably linked to, or associated with, a nucleotide sequence that codes for an mRNA or which is expressed as a polypeptide, such that the regulatory nucleotide sequence is able to regulate transcription or expression of the associated nucleotide sequence. The regulatory nucleotide sequence of the chimeric construct is not normally operably linked to the associated nucleotide sequence as found in nature.

As used herein, the terms “coding sequence” and “open reading frame” (ORF) are used interchangeably and refer to a nucleotide sequence that is transcribed into RNA such as mRNA, rRNA, tRNA, snRNA, sense RNA, or antisense RNA. In some embodiments, the RNA is then translated in vivo or in vitro to produce a polypeptide. In some embodiments, an ORF of a maize Q protein comprises SEQ ID NO: 1.

As used herein, the term “complementary” refers to two nucleotide sequences that comprise antiparallel nucleotide sequences capable of pairing with one another upon formation of hydrogen bonds between the complementary base residues in the antiparallel nucleotide sequences. As is known in the art, the nucleotide sequences of two complementary strands are the reverse complement of each other when each is viewed in the 5′ to 3′ direction.

As is also known in the art, two sequences that hybridize to each other under a given set of conditions do not necessarily have to be 100% fully complementary. As used herein, the terms “fully complementary” and “100% complementary” refer to sequences for which the complementary regions are 100% in Watson-Crick base-pairing: i.e., that no mismatches occur within the complementary regions. However, as is often the case with recombinant molecules (for example, cDNAs) that are cloned into cloning vectors, certain of these molecules can have non-complementary overhangs on either the 5′ or 3′ ends that result from the cloning event. In such a situation, it is understood that the region of 100% or full complementarity excludes any sequences that are added to the recombinant molecule (typically at the ends) solely as a result of, or to facilitate, the cloning event. Such sequences are, for example, polylinker sequences, linkers with restriction enzyme recognition sites, etc.

As used herein, the terms “domain” and “feature”, when used in reference to a polypeptide or amino acid sequence, refers to a subsequence of an amino acid sequence that has a particular biological function. Domains and features that have a particular biological function include, but are not limited to, a signal sequence, a ligand binding domain, a nucleic acid binding domain, a catalytic domain, a substrate binding domain, and a polypeptide-polypeptide interacting domain. Similarly, when used herein in reference to a nucleotide sequence, a “domain”, or “feature” is that subsequence of the nucleotide sequence that encodes a domain or feature of a polypeptide.

As used herein, the term “expression cassette” refers to a nucleic acid molecule capable of directing expression of a particular nucleotide sequence in an appropriate host cell, comprising a promoter operably linked to the nucleotide sequence of interest which is operably linked to termination signals. It also typically comprises sequences required for proper translation of the nucleotide sequence. The coding region usually encodes a polypeptide of interest but can also encode a functional RNA of interest, for example antisense RNA or a non-translated RNA, in the sense or antisense direction. The expression cassette comprising the nucleotide sequence of interest can be chimeric, meaning that at least one of its components is heterologous with respect to at least one of its other components. The expression cassette can also be one that is naturally occurring but has been obtained in a recombinant form useful for heterologous expression. Typically, however, at least one component of the expression cassette is heterologous with respect to the host; for example, a particular DNA sequence of the expression cassette does not occur naturally in the host cell and was introduced into the host cell or an ancestor of the host cell by a transformation event. The expression of the nucleotide sequence in the expression cassette can be under the control of a promoter (for example, the Q protein promoter of SEQ ID NO: 6), and in some embodiments, a promoter that initiates transcription only when the host cell is exposed to some particular external stimulus. In the case of a multicellular organism such as a plant, the promoter can also be specific to a particular tissue, organ, or stage of development (for example, a plant seed).

As used herein, the term “fragment” refers to a sequence that comprises a subset of another sequence. When used in the context of a nucleic acid or amino acid sequence, the terms “fragment” and “subsequence” are used interchangeably. A fragment of a nucleotide sequence can be any number of nucleotides that is less than that found in another nucleotide sequence, and thus includes, but is not limited to, the sequences of an exon or intron, a promoter, an enhancer, an origin of replication, a 5′ or 3′ untranslated region, a coding region, and a polypeptide binding domain. It is understood that a fragment or subsequence can also comprise less than the entirety of a nucleotide sequence, for example, a portion of an exon or intron, promoter, enhancer, etc. Similarly, a fragment or subsequence of an amino acid sequence can be any number of residues that is less than that found in a naturally occurring polypeptide, and thus includes, but is not limited to, domains, features, repeats, etc. Also similarly, it is understood that a fragment or subsequence of an amino acid sequence need not comprise the entirety of the amino acid sequence of the domain, feature, repeat, etc. A fragment can also be a “functional fragment”, in which the fragment retains a specific biological function of the nucleotide sequence or amino acid sequence of interest. For example, a functional fragment of a transcription factor can include, but is not limited to, a DNA binding domain, a transactivating domain, or both. Similarly, a functional fragment of a receptor tyrosine kinase can include, but is not limited to, a ligand binding domain, a kinase domain, an ATP binding domain, and combinations thereof.

As used herein, the term “gene” is used broadly to refer to any segment of DNA associated with a biological function. Thus, genes include, but are not limited to, coding sequences and/or the regulatory sequences required for their expression. Genes can also include non-expressed DNA segments that, for example, form recognition sequences for a polypeptide. Genes can be obtained from a variety of sources, including cloning from a source of interest or synthesizing from known or predicted sequence information, and can include sequences designed to have desired parameters.

The terms “heterologous” and “recombinant”, when used herein to refer to a nucleotide sequence (e.g. a DNA sequence) or a gene, refer to a sequence that originates from a source foreign to the particular host cell or, if from the same source, is modified from its original form. Thus, a heterologous gene in a host cell includes a gene that is endogenous to the particular host cell but has been modified through, for example, the use of DNA shuffling or other recombinant techniques. The terms also include non-naturally occurring multiple copies of a naturally occurring DNA sequence. Thus, the terms refer to a DNA segment that is foreign to the host cell, or naturally occurring in the host cell but in a position or form within the host cell in which the element is not ordinarily found in nature. Similarly, when used in the context of a polypeptide or amino acid sequence, a heterologous polypeptide or amino acid sequence is a polypeptide or amino acid sequence that originates from a source foreign to the particular host cell (e.g., is generated from a heterologous coding sequence) or, if from the same source, is modified from its original form. Thus, heterologous DNA segments can be expressed to yield heterologous polypeptides.

A “homologous” nucleotide (or amino acid) sequence is a nucleotide (or amino acid) sequence naturally associated with a host cell into which it is introduced and that is present in the chromosomal or extrachromosomal position in which it is normally found in nature.

The phrase “hybridizing specifically to” refers to the binding, duplexing, or hybridizing of a molecule only to a particular nucleotide sequence under stringent conditions when that sequence is present in a complex mixture (e.g., total cellular) DNA or RNA. The phrase “bind(s) substantially” refers to complementary hybridization between a probe nucleic acid and a target nucleic acid and embraces minor mismatches that can be accommodated by reducing the stringency of the hybridization media to achieve the desired detection of the target nucleotide sequence.

As used herein, the terms “mutation” and “mutant” carry their traditional connotations and refer to a change, inherited, naturally occurring, or introduced, in a nucleic acid or polypeptide sequence, and are used in their senses as generally known to those of skill in the art.

As used herein, the term “inhibitor” refers to a chemical substance that inactivates or decreases the biological activity of a polypeptide such as a biosynthetic and catalytic activity, receptor, signal transduction polypeptide, structural gene product, or transport polypeptide. The term “herbicide” (or “herbicidal compound”) is used herein to define an inhibitor applied to a plant at any stage of development, whereby the herbicide inhibits the growth of the plant or kills the plant.

As used herein, the term “isolated”, when used in the context of an isolated DNA molecule or an isolated polypeptide, is a DNA molecule or polypeptide that, by the hand of man, exists apart from its native environment and is therefore not a product of nature. An isolated DNA molecule or polypeptide can exist in a purified form or can exist in a non-native environment such as, for example, in a transgenic host cell.

As used herein, the term “mature polypeptide” refers to a polypeptide from which the transit peptide, signal peptide, and/or propeptide portions have been removed.

As used herein, the term “minimal promoter” refers to the smallest piece of a promoter, such as a TATA element, that can support any transcription. A minimal promoter typically has greatly reduced promoter activity in the absence of upstream or downstream activation. In the presence of a suitable transcription factor, a minimal promoter can function to permit transcription.

As used herein, the terms “cell”, “cell line”, and “cell culture” are used interchangeably, and all such designations include progeny. Thus, the words “transformants” and “transformed cells” include the primary subject cell and cultures derived therefrom without regard for the number of transfers and/or rounds of cell division that the originally manipulated cell or cells might have experienced. It is also understood that all progeny might not be precisely identical in DNA content, due to deliberate or inadvertent mutations. Mutant progeny that have the same function or biological activity as screened for in the originally transformed cell are encompassed by the terms. Where distinct designations are intended, it will be clear from the context.

As used herein, the term “native” refers to a gene that is naturally present in the genome of an untransformed plant cell. Similarly, when used in the context of a polypeptide, a “native polypeptide” is a polypeptide that is encoded by a native gene of an untransformed plant cell's genome.

As used herein, the term “naturally occurring” refers to an object that is found in nature as distinct from being artificially produced by man. For example, a polypeptide or nucleotide sequence that is present in an organism in its natural state, which has not been intentionally modified or isolated by man in the laboratory, is naturally occurring. As such, a polypeptide or nucleotide sequence is considered “non-naturally occurring” if it is encoded by or present within a recombinant molecule, even if the amino acid or nucleotide sequence is identical to an amino acid or nucleotide sequence found in nature.

As used herein, the term “nucleic acid” refers to deoxyribonucleotides or ribonucleotides and polymers thereof in either single- or double-stranded form. Unless specifically limited, the term encompasses nucleic acids containing known analogues of natural nucleotides that have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides. Unless otherwise indicated, a particular nucleotide sequence also implicitly encompasses conservatively modified variants thereof (e.g. degenerate codon substitutions) and complementary sequences and as well as the sequence explicitly disclosed. Specifically, degenerate codon substitutions can be achieved by generating sequences in which the third position of one or more (or all) selected codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al., 1991; Ohtsuka et al., 1985; Rossolini et al., 1994). The terms “nucleic acid” or “nucleotide sequence” can also be used interchangeably with gene, cDNA, and mRNA encoded by a gene.

As used herein, the term “orthologs” refers to genes in different species that encode protein that perform the same biological function. For example, the glucose-6-phosphate dehydrogenase genes from, for example, sorghum and rice, are orthologs. Typically, orthologous nucleotide sequences are characterized by a high degree of sequence similarity (for example, at least about 90% sequence identity). A nucleotide sequence of an ortholog in one species (for example, rice) can be used to isolate the nucleotide sequence of the ortholog in another species (for example, sorghum) using standard molecular biology techniques. This can be accomplished, for example, using techniques described in more detail below (see also Sambrook & Russell, 2001 for a discussion of hybridization conditions that can be used to isolate closely related sequences).

As used herein, the phrase “percent identical”, “in the context of two nucleic acid or polypeptide sequences, refers to two or more sequences or subsequences that have in some embodiments 60% (e.g., 60, 63, 65, 67, or 69%), in some embodiments 70% (e.g., 70, 73, 75, 77, or 79%), in some embodiments 80% (e.g., 80, 83, 85, 87, or 89%), in some embodiments 90% (e.g., 90, 93, 95, or 97), and in some embodiments at least 99% nucleotide or amino acid residue identity, respectively, when compared and aligned for maximum correspondence, as measured using one of the following sequence comparison algorithms or by visual inspection. The percent identity exists in some embodiments over a region of the sequences that is at least about 50 residues in length, in some embodiments over a region of at least about 100 residues, and In some embodiments, the percent identity exists over at least about 150 residues. In some embodiments, the percent identity exists over the entire length of the sequences.

For sequence comparison, typically one sequence acts as a reference sequence to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are input into a computer, subsequence coordinates are designated if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.

Optimal alignment of sequences for comparison can be conducted, for example, by the local homology algorithm disclosed in Smith & Waterman, 1981, by the homology alignment algorithm disclosed in Needleman & Wunsch, 1970, by the search for similarity method disclosed in Pearson & Lipman, 1988, by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the GCG® WISCONSIN PACKAGE®, available from Accelrys, Inc., San Diego, Calif., United States of America), or by visual inspection. See generally, Ausubel et al., 2002; Ausubel et al., 2003.

One example of an algorithm that is suitable for determining percent sequence identity and sequence similarity is the BLAST algorithm, which is described in Altschul et al., 1990. Software for performing BLAST analysis is publicly available through the website of the National Center for Biotechnology Information. This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold. See generally, Altschul et al., 1990. These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when the cumulative alignment score falls off by the quantity X from its maximum achieved value, the cumulative score goes to zero or below due to the accumulation of one or more negative-scoring residue alignments, orthe end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, a cutoff of 100, M=5, N==4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix. See Henikoff & Henikoff, 1992.

In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see e.g., Karlin & Altschul, 1993). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a test nucleotide sequence is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleotide sequence to the reference nucleotide sequence is in some embodiments less than about 0.1, in some embodiments less than about 0.01, and in some embodiments less than about 0.001.

As used herein, the terms “Q protein”, “55 kDa protein”, “55 kDa Q protein”, and “55 kDa maize protein” are used interchangeably and refer to a polypeptide comprising the amino acid sequence of SEQ ID NO: 2, and variants, fragments, and domains thereof. A representative open reading frame for this polypeptide sequence has been identified, and has the nucleotide sequence provided in SEQ ID NO: 1. Additionally, a region of the maize promoter that controls transcription of this coding sequence in maize, referred to alternatively herein as the “Q protein gene promoter”, the “promoter from the Q protein gene”, etc., has been identified, and comprises the nucleotide sequence presented in SEQ ID NO: 6.

As used herein, the term “shuffled nucleic acid” refers to a recombinant nucleic acid molecule in which the nucleotide sequence comprises a plurality of nucleotide sequence fragments, wherein at least one of the fragments corresponds to a region of a nucleotide sequence listed in SEQ ID NO: 1, and wherein at least two of the plurality of sequence fragments are in an order, from 5′ to 3′, which is not an order in which the plurality of fragments naturally occur in a nucleic acid.

The term “substantially identical”, in the context of two nucleotide or amino acid sequences, refers to two or more sequences or subsequences that have in some embodiments at least about 60% nucleotide or amino acid identity (e.g., 60, 63, 65, 67, or 69% nucleotide or amino acid identity), in some embodiments at least about 70% nucleotide or amino acid identity (e.g., 70, 73, 75, 78, or 79% nucleotide or amino acid identity), in some embodiments at least about 80% nucleotide or amino acid identity (e.g., 80, 83, 85, 88, or 89% nucleotide or amino acid identity), and in some embodiments at least about 90% nucleotide or amino acid identity (e.g., 90, 93, 95, 98, or 99% nucleotide or amino acid identity), when compared and aligned for maximum correspondence, as measured using one of the above-referenced sequence comparison algorithms or by visual inspection. In some embodiments, the substantial identity exists in nucleotide or amino acid sequences of at least 50 residues, in some embodiments in nucleotide or amino acid sequence of at least about 100 residues, in some embodiments in nucleotide or amino acid sequences of at least about 150 residues, and in some embodiments in nucleotide or amino acid sequences comprising complete coding sequences or complete amino acid sequences.

In one aspect, polymorphic sequences can be substantially identical sequences. The term “polymorphic” refers to the two or more genetically determined alternative sequences or alleles in a population. An allelic difference can be as small as one base pair. Nonetheless, one of ordinary skill in the art would recognize that the polymorphic sequences correspond to the same gene.

Another indication that two nucleotide sequences are substantially identical is that the two molecules specifically or substantially hybridize to each other under conditions of medium or high stringency. In the context of nucleic acid hybridization, two nucleotide sequences being compared can be designated a “probe sequence” and a “target sequence”. A “probe sequence” is a reference nucleic acid molecule, and a “target sequence” is a test nucleic acid molecule, often found within a heterogeneous population of nucleic acid molecules. A “target sequence” is synonymous with a “test sequence”.

An exemplary nucleotide sequence employed for hybridization studies or assays includes probe sequences that are complementary to or mimic in some embodiments at least an about 14 to 40 nucleotide sequence of a nucleic acid molecule of the presently disclosed subject matter. In some embodiments, probes comprise 14 to 20 nucleotides, or even longer where desired, such as 30, 40, 50, 60, 100, 200, 300, or 500 nucleotides or up to the full length (for example, the full complement) of any of the nucleotide sequence set forth in the SEQ ID NO: 1. Such fragments can be readily prepared by, for example, directly synthesizing the fragment by chemical synthesis, by application of nucleic acid amplification technology, or by introducing selected sequences into recombinant vectors for recombinant production.

The phrase “hybridizing substantially to” refers to complementary hybridization between a probe nucleic acid molecule and a target nucleic acid molecule and embraces minor mismatches (for example, polymorphisms) that can be accommodated by reducing the stringency of the hybridization and/or wash media to achieve the desired hybridization.

“Stringent hybridization conditions” and “stringent hybridization wash conditions” in the context of nucleic acid hybridization experiments such as Southern and Northern blot analysis are both sequence- and environment-dependent. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen, 1993. Generally, high stringency hybridization and wash conditions are selected to be about 5° C. lower than the thermal melting point (T_(m)) for the specific sequence at a defined ionic strength and pH. Typically, under “highly stringent conditions” a probe will hybridize specifically to its target subsequence, but to no other sequences. Similarly, medium stringency hybridization and wash conditions are selected to be more than about 5° C. lower than the T_(m) for the specific sequence at a defined ionic strength and pH. Exemplary medium stringency conditions include hybridizations and washes as for high stringency conditions, except that the temperatures for the hybridization and washes are in some embodiments 8° C., in some embodiments 10° C., in some embodiments 12° C., and in some embodiments 15° C. lower than the T_(m) for the specific sequence at a defined ionic strength and pH.

The T_(m) is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Very stringent conditions are selected to be equal to the T_(m) for a particular probe. An example of highly stringent hybridization conditions for Southern or Northern Blot analysis of complementary nucleic acids having more than about 100 complementary residues is overnight hybridization in 6× standard saline citrate (SSC) or standard saline-phosphate-EDTA (SSPE) at 65° C. (or at 42° C. if 50% formamide is included in the hybridization buffer) containing 5× Denhardt's reagent, 0.5% sodium dodecyl sulfate (SDS), 1 μg/ml poly(A), and 100 μg/ml salmon sperm DNA (50× Denhardt's reagent is 1% (w/v) Ficoll 400, 1% (w/v) polyvinylpyrrolidone, and 1% (w/v) bovine serum albumin; see Sambrook and Russell, 2001, for alternative hybridization and wash conditions and solutions that can be used for the same). An example of highly stringent wash conditions is 15 minutes in 0.1×SSC, 0.1% (w/v) SDS at 65° C. Another example of highly stringent wash conditions is 15 minutes in 0.2×SSC buffer at 65° C. Often, a high stringency wash is preceded by a lower stringency wash to remove background probe signal. An example of medium stringency wash conditions for a duplex of more than about 100 nucleotides is 15 minutes in 1×SSC at 45-55° C. Another example of medium stringency wash for a duplex of more than about 100 nucleotides is 15 minutes in 4-6×SSC at 40° C. For short probes (e.g., about 10 to 50 nucleotides), stringent conditions typically involve salt concentrations of less than about 1 M Na⁺ ion, typically about 0.01 to 1 M Na⁺ ion concentration (or other salts) at pH 7.0-8.3, and the temperature is typically at least about 30° C. Stringent conditions can also be achieved with the addition of destabilizing agents such as formamide. In general, a signal to noise ratio of 2-fold (or higher) than that observed for an unrelated probe in the particular hybridization assay indicates detection of a specific hybridization.

The following are examples of hybridization and wash conditions that can be used to clone homologous nucleotide sequences that are substantially identical to reference nucleotide sequences of the presently disclosed subject matter: in some embodiments, a probe and target sequence hybridizes in 7% SDS, 0.5M NaPO₄, 1 mm ethylene diamine tetraacetic acid (EDTA) at 50° C. followed by washing in 2×SSC, 0.1% SDS at 50° C.; in some embodiments, a probe and target sequence hybridize in 7% SDS, 0.5 M NaPO₄, 1 mm EDTA at 50° C. followed by washing in 1×SSC, 0.1% SDS at 50° C.; in some embodiments, a probe and target sequence hybridize in 7% SDS, 0.5 M NaPO₄, 1 mm EDTA at 50° C. followed by washing in 0.5×SSC, 0.1% SDS at 50° C.; in some embodiments, a probe and target sequence hybridize in 7% SDS, 0.5 M NaPO₄, 1 mm EDTA at 50° C. followed by washing in 0.1×SSC, 0.1% SDS at 50° C.; in some embodiments, a probe and target sequence hybridize in 7% SDS, 0.5 M NaPO₄, 1 mm EDTA at 50° C. followed by washing in 0.1×SSC, 0.1% SDS at 55° C.; in some embodiments, a probe and target sequence hybridize in 7% SDS, 0.5 M NaPO₄, 1 mm EDTA at 50° C. followed by washing in 0.1×SSC, 0.1% SDS at 60° C.; and in some embodiments, a probe and target sequence hybridize in 7% SDS, 0.5 M NaPO₄, 1 mm EDTA at 50° C. followed by washing in 0.1×SSC, 0.1% SDS at 65° C. In some embodiments, hybridization conditions comprise hybridization in a roller tube for at least 12 hours at 42° C. in 7% SDS, 0.5 M NaPO₄, 1 mm EDTA.

As used herein, the term “pre-polypeptide” refers to a polypeptide that is normally targeted to a cellular organelle, such as a chloroplast, and still comprises a transit peptide.

As used herein, the term “purified”, when applied to a nucleic acid or polypeptide, denotes that the nucleic acid or polypeptide is essentially free of other cellular components with which it is associated in the natural state. It can be in a homogeneous state although it can be in either a dry or aqueous solution. Purity and homogeneity are typically determined using analytical chemistry techniques such as polyacrylamide gel electrophoresis or high performance liquid chromatography. A polypeptide that is the predominant species present in a preparation is substantially purified. The term “purified” denotes that a nucleic acid or polypeptide gives rise to essentially one band in an electrophoretic gel. Particularly, it means that the nucleic acid or polypeptide is in some embodiments at least about 50% pure, in some embodiments at least about 85% pure, and in some embodiments at least about 99% pure.

Two nucleic acids are “recombined” when sequences from each of the two nucleic acids are combined in a progeny nucleic acid. Two sequences are “directly” recombined when both of the nucleic acids are substrates for recombination. Two sequences are “indirectly recombined” when the sequences are recombined using an intermediate such as a cross-over oligonucleotide. For indirect recombination, no more than one of the sequences is an actual substrate for recombination, and in some cases, neither sequence is a substrate for recombination.

As used herein, the term “regulatory elements” refers to nucleotide sequences involved in controlling the expression of a nucleotide sequence. Regulatory elements can comprise a promoter operably linked to the nucleotide sequence of interest and termination signals. Regulatory sequences also include enhancers and silencers. They also typically encompass sequences required for proper translation of the nucleotide sequence.

As used herein, the term “transformation” refers to a process for introducing heterologous DNA into a plant cell, plant tissue, or plant. Transformed plant cells, plant tissue, or plants are understood to encompass not only the end product of a transformation process, but also transgenic progeny thereof.

As used herein, the terms “transformed”, “transgenic”, and “recombinant” refer to a host cell or organism such as a bacterium or a plant cell (e.g., a plant) into which a heterologous nucleic acid molecule has been introduced. The nucleic acid molecule can be stably integrated into the genome of the host or the nucleic acid molecule can also be present as an extrachromosomal molecule. Such an extrachromosomal molecule can be auto-replicating. Transformed cells, tissues, or plants are understood to encompass not only the end product of a transformation process, but also transgenic progeny thereof. A “non-transformed,” “non-transgenic”, or “non-recombinant” host refers to a wild-type organism, e.g., a bacterium or plant, which does not contain the heterologous nucleic acid molecule.

As used herein, the term “heterologous” as it relates to a nucleotide sequence (or an amino acid sequence encoded thereby) refers not only to a nucleic acid or amino acid sequence that is derived from a species other than the species into which it is introduced, but also refers to a nucleotide sequence from the same species that is manipulated in the genome of a cell or organism of that species such that the genome contains some man made alteration.

Thus, the term “transgenic” refers not only to a cell of Zea mays, for example, that comprises a nucleic acid molecule that is not naturally occurring in Zea mays, but also includes a cell of Zea mays, for example, that comprises a nucleic acid molecule all or parts of which are naturally occurring in Zea mays, but have been modified in some form such that the genome of the transgenic plant is identifiably different from that of a naturally occurring Zea mays. In some embodiments, the modification comprises introducing one or more additional copies of a Zea mays nucleotide sequence into a Zea mays cell. In some embodiments, the modification comprises “knocking in” a heterologous nucleotide sequence into the Q protein gene, such that the heterologous nucleotide sequence becomes operably linked to the endogenous Q protein gene promoter.

III. Nucleic Acid Molecules and Polypeptides

III.A. Nucleic Acid Molecules

Embodiments of the presently disclosed subject matter encompass isolated nucleic acid molecules corresponding to members of the prolamin family of Zea mays cereal seed storage proteins, and a nucleotide sequence from the promoter region of one such family member that can be used to control expression of operably linked nucleotide sequences. In some embodiments, an isolated nucleic acid molecule of the presently disclosed subject matter comprises a nucleotide sequence that hybridizes under highly stringent conditions of hybridization of 65° C. in 6×SSC, followed by a final washing step of at least 15 minutes at 65° C. in 0.1×SSC to a nucleotide sequence as set forth in SEQ ID NO: 1, or a fragment, domain, or feature thereof. In some embodiments, an isolated nucleic acid molecule of the presently disclosed subject matter comprises a nucleotide sequence having substantial identity to a nucleotide sequence that hybridizes under highly stringent conditions of hybridization of 65° C. in 6×SSC, followed by a final washing step of at least 15 minutes at 65° C. in 0.1×SSC to a nucleotide sequence as set forth in SEQ ID NO: 1, or a fragment, domain, or feature thereof. In some embodiments, the presently disclosed subject matter encompasses an isolated nucleic acid molecule comprising a nucleotide sequence that is complementary to, or the reverse complement of, a nucleotide sequence that hybridizes under highly stringent conditions of hybridization of 65° C. in 6×SSC, followed by a final washing step of at least 15 minutes at 65° C. in 0.1×SSC to a nucleotide sequence listed in SEQ ID NO: 1, or a fragment, domain, or feature thereof. Some embodiments of the presently disclosed subject matter encompass an isolated nucleic acid molecule comprising a nucleotide sequence that is complementary to, or the reverse complement of, a nucleotide sequence that has substantial identity to, or is capable of hybridizing to, a nucleotide sequence that hybridizes under highly stringent conditions of hybridization of 65° C. in 6×SSC, followed by a final washing step of at least 15 minutes at 65° C. in 0.1×SSC to a nucleotide sequence listed in SEQ ID NO: 1, or a fragment, domain, or feature thereof.

In some embodiments, the substantial identity is at least about 60% identity (e.g., 60, 63, 65, 67, or 69% identity), in some embodiments at least about 70% identity (e.g., 70, 73, 75, 77, or 79% identity), in some embodiments about 80% identity (e.g., 80, 83, 85, 87, or 89% identity), in some embodiments about 90% identity (e.g., 90 or 93% identity), in some embodiments about 95% identity, in some embodiments about 97% identity, and in some embodiments at least about 99% identity to the nucleotide sequence listed in SEQ ID NO: 1, or a fragment, domain, or feature thereof.

In some embodiments, the nucleotide sequence having substantial identity comprises an allelic variant of the nucleotide sequence that hybridizes under highly stringent conditions of hybridization of 65° C. in 6×SSC, followed by a final washing step of at least 15 minutes at 65° C. in 0.1×SSC to a nucleotide sequence listed in SEQ ID NO: 1, or a fragment, domain, or feature thereof. In some embodiments, the nucleotide sequence having substantial identity comprises a naturally occurring variant. In some embodiments, the nucleotide sequence having substantial identity comprises a polymorphic variant of the nucleotide sequence that hybridizes under highly stringent conditions of hybridization of 65° C. in 6×SSC, followed by a final washing step of at least 15 minutes at 65° C. in 0.1×SSC to a nucleotide sequence listed in SEQ ID NO: 1, or a fragment, domain, or feature thereof.

In some embodiments, the nucleic acid having substantial identity comprises a deletion or insertion of at least one nucleotide. In some embodiments, the deletion or insertion comprises less than about thirty nucleotides. In some embodiments, the deletion or insertion comprises less than about five nucleotides. In some embodiments, the sequence of the isolated nucleic acid having substantial identity comprises a substitution in at least one codon. In some embodiments, the substitution is conservative.

In some embodiments, the isolated nucleic acid comprises a plurality of regions having a nucleotide sequence that hybridizes under highly stringent conditions of hybridization of 65° C. in 6×SSC, followed by a final washing step of at least 15 minutes at 65° C. in 0.1×SSC to a nucleotide sequence listed in SEQ ID NO: 1, or an exon, domain, or feature thereof.

In some embodiments, the sequence having substantial identity to the nucleotide sequence that hybridizes under highly stringent conditions of hybridization of 65° C. in 6×SSC, followed by a final washing step of at least 15 minutes at 65° C. in 0.1×SSC to a nucleotide sequence listed in SEQ ID NO: 1, or a fragment, domain, or feature thereof, is from a plant. In some embodiments, the plant is a dicot. In some embodiments, the plant is a gymnosperm. In some embodiments, the plant is a monocot. In some embodiments, the monocot is a cereal. In some embodiments, the cereal can be, for example, maize, wheat, barley, oats, rye, millet, sorghum, triticale, secale, einkorn, spelt, emmer, teff, milo, flax, gramma grass, Tripsacum sp., or teosinte. In some embodiments, the cereal is rice.

In some embodiments, the nucleic acid is expressed in a specific location or tissue of a plant. In some embodiments, the location or tissue includes, but is not limited to, epidermis, root, vascular tissue, meristem, cambium, cortex, pith, leaf, flower, see, and combinations thereof. In some embodiments, the location or tissue is a seed. In some embodiments, the location or tissue is a protein body of a seed.

Embodiments of the presently disclosed subject matter also relate to a shuffled nucleic acid molecule comprising a plurality of nucleotide sequence fragments, wherein at least one of the fragments corresponds to a region of a nucleotide sequence that hybridizes under highly stringent conditions of hybridization of 65° C. in 6×SSC, followed by a final washing step of at least 15 minutes at 65° C. in 0.1×SSC to a nucleotide sequence listed in SEQ ID NO: 1, and wherein at least two of the plurality of sequence fragments are in an order, from 5′ to 3′, which is not an order in which the plurality of fragments naturally occur. In some embodiments, all of the fragments in a shuffled nucleic acid comprising a plurality of nucleotide sequence fragments are from a single gene. In some embodiments, the plurality of fragments is derived from at least two different genes. In some embodiments, the shuffled nucleic acid is operably linked to a promoter sequence. In some embodiments, the shuffled nucleic acid comprises a chimeric polynucleotide comprising a promoter sequence operably linked to the shuffled nucleic acid. In some embodiments, the shuffled nucleic acid is contained within a host cell.

III.B. Identifying, Cloning, and Sequencing cDNAs

The cloning and sequencing of the cDNAs of the presently disclosed subject matter is accomplished using techniques known in the art. See generally, Sambrook & Russell, 2001; Silhavy et al., 1984; Ausubel et al., 2002; Ausubel et al., 2003; Reiter et al., 1992; Schultz et al., 1998.

The isolated nucleic acids and polypeptides of the presently disclosed subject matter are usable over a range of plants—monocots and dicots—in particular monocots such as sorghum, rice, wheat, barley, and maize. In some embodiments, the monocot is a cereal. In some embodiments, the cereal can be, for example, maize, wheat, barley, oats, rye, millet, sorghum, triticale, secale, einkorn, spelt, emmer, teff, milo, flax, gramma grass, Tripsacum sp., or teosinte. In some embodiments, the cereal is maize. Other plant genera relevant to the presently disclosed subject matter include, but are not limited to, Cucurbita, Rosa, Vitis, Juglans, Gragaria, Lotus, Medicago, Onobrychis, Trigonella, Vigna, Citrus, Linum, Geranium, Manihot, Daucus, Arabidopsis, Brassica, Raphanus, Sinapis, Atropa, Capsicum, Datura, Hyoscyamus, Lycopersicon, Nicotiana, Solanum, Petunia, Digitalis, Majorana, Ciahorium, Helianthus, Lactuca, Bromus, Asparagus, Antirrhinum, Heterocallis, Nemesis, Pelargonium, Panieum, Pennisetum, Ranunculus, Senecio, Salpiglossis, Cucumis, Browaalia, Glycine, Pisum, Phaseolus, Lolium, Oryza, Avena, Hordeum, Secale, Allium, and Triticum.

The presently disclosed subject matter also provides a method for genotyping a plant or plant part comprising a nucleic acid molecule of the presently disclosed subject matter. Optionally, the plant is a monocot such as, but not limited to, sorghum, rice, maize, or wheat. Genotyping provides a methodology for distinguishing homologs of a chromosome pair and can be used to differentiate segregants in a plant population. Molecular marker methods can be used in phylogenetic studies, characterizing genetic relationships among crop varieties, identifying crosses or somatic hybrids, localizing chromosomal segments affecting monogenic traits, mapping based cloning, and the study of quantitative inheritance (see Clark, 1997; Paterson, 1996).

The method for genotyping can employ any number of molecular marker analytical techniques including, but not limited to, restriction length polymorphisms (RFLPs). As is well known in the art, RFLPs are produced by differences in the DNA restriction fragment lengths resulting from nucleotide differences between alleles of the same gene. Thus, the presently disclosed subject matter provides a method for following segregation of a gene or nucleic acid of the presently disclosed subject matter or chromosomal sequences genetically linked by using RFLP analysis. Linked chromosomal sequences are in some embodiments within 50 centimorgans (cM), in some embodiments within 40 cM, in some embodiments within 30 cM, in some embodiments within 20 cM, in some embodiments within 10 cM, and in some embodiments within 5, 3, 2, or 1 cM of the nucleic acid of the presently disclosed subject matter.

Embodiments of the presently disclosed subject matter also relate to an isolated nucleic acid molecule comprising a nucleotide sequence, its complement (for example, its full complement), or its reverse complement (for example, its full reverse complement), the nucleotide sequence encoding a polypeptide (for example, a biologically active polypeptide or biologically active fragment). In some embodiments, the nucleotide sequence encodes a polypeptide that is an ortholog of a polypeptide comprising a polypeptide sequence listed in SEQ ID NO: 2, or a fragment, domain, repeat, feature, or chimera thereof. In some embodiments, the nucleotide sequence encodes a polypeptide that is an ortholog of a polypeptide comprising a polypeptide sequence having substantial identity to a polypeptide sequence listed in SEQ ID NO: 2, or a fragment, domain, repeat, feature, or chimera thereof. In some embodiments, the nucleotide sequence encodes a polypeptide that is an ortholog of a polypeptide comprising a polypeptide sequence encoded by a nucleotide sequence identical to or having substantial identity to a nucleotide sequence listed in SEQ ID NO: 1, or a fragment, domain, orfeature thereof, or a sequence complementary thereto. In some embodiments, the nucleotide sequence encodes a polypeptide comprising a polypeptide sequence encoded by a nucleotide sequence that hybridizes under highly stringent conditions of hybridization of 65° C. in 6×SSC, followed by a final washing step of at least 15 minutes at 65° C. in 0.1×SSC to a nucleotide sequence listed in SEQ ID NO: 1, or to a sequence complementary thereto. In some embodiments, the nucleotide sequence encodes a functional fragment of a polypeptide of the presently disclosed subject matter.

In some embodiments, the isolated nucleic acid comprises a polypeptide-encoding sequence. In some embodiments, the polypeptide-encoding sequence encodes a polypeptide that is an ortholog of a polypeptide comprising a polypeptide sequence listed in SEQ ID NO: 2, or a fragment thereof. In some embodiments, the polypeptide is a plant polypeptide. In some embodiments, the plant is a dicot. In some embodiments, the plant is a gymnosperm. In some embodiments, the plant is a monocot. In some embodiments, the monocot is a cereal. In some embodiments, the cereal includes, but is not limited to, maize, wheat, barley, oats, rye, millet, sorghum, triticale, secale, einkorn, spelt, emmer, teff, miloflax, gramma grass, Tripsacum, and teosinte. In some embodiments, the cereal is maize.

Embodiments of the presently disclosed subject matter also relate to an isolated nucleic acid molecule comprising a nucleotide sequence, its complement (for example, its full complement), or its reverse complement (for example, its full reverse complement), encoding a polypeptide selected from a group comprising one or more of:

-   -   (a) a polypeptide sequence encoded by a nucleotide sequence that         hybridizes under highly stringent conditions of hybridization of         65° C. in 6×SSC, followed by a final washing step of at least 15         minutes at 65° C. in 0.1×SSC to a nucleotide sequence listed in         SEQ ID NO: 1, or a fragment, domain, or feature thereof, or a         sequence complementary thereto; and     -   (b) a functional fragment of (a).

In some embodiments, the polypeptide having substantial identity comprises an allelic variant of a polypeptide that is an ortholog of a polypeptide having an amino acid sequence listed in SEQ ID NO: 2, or a fragment, domain, repeat, feature, or chimera thereof. In some embodiments, the isolated nucleic acid comprises a plurality of regions from the polypeptide sequence encoded by a nucleotide sequence that hybridizes under highly stringent conditions of hybridization of 65° C. in 6×SSC, followed by a final washing step of at least 15 minutes at 65° C. in 0.1×SSC to a nucleotide sequence listed in SEQ ID NO: 1, or a fragment, domain, or feature thereof, or a sequence complementary thereto.

III.C. Polypeptides

The presently disclosed subject matter further relates to isolated polypeptides that are orthologs of the polypeptide comprising the amino acid sequences set forth in SEQ ID NO: 2, including biologically active polypeptides. In some embodiments, the polypeptide comprises a polypeptide sequence of an ortholog of a polypeptide listed in SEQ ID NO: 2. In some embodiments, the polypeptide comprises a functional fragment or domain of an ortholog of a polypeptide comprising a polypeptide sequence listed in SEQ ID NO: 2. In some embodiments, the polypeptide comprises a chimera of an ortholog of the polypeptide sequence listed in SEQ ID NO: 2, where the chimera can comprise functional polypeptide motifs, including domains, repeats, post-translational modification sites, or other features. In some embodiments, the polypeptide is a plant polypeptide. In some embodiments, the plant is a dicot. In some embodiments, the plant is a gymnosperm. In some embodiments, the plant is a monocot. In some embodiments, the monocot is a cereal. In some embodiments, the cereal is, for example, maize, wheat, barley, oats, rye, millet, sorghum, triticale, secale, einkorn, spelt, emmer, teff, milo, flax, gramma grass, Tripsacum, or teosinte. In some embodiments, the cereal is maize.

In some embodiments, the polypeptide is expressed in a specific location or tissue of a plant. In some embodiments, the location or tissue includes, but is not limited to, epidermis, root, vascular tissue, meristem, cambium, cortex, pith, leaf, flower, seed, and combinations thereof. In some embodiments, the location or tissue is a seed. In some embodiments, the location or tissue is a protein body of a seed.

In some embodiments, isolated polypeptides comprise the amino acid sequences of orthologs of the polypeptides comprising the amino acid sequence set forth in SEQ ID NO: 2, and variants having conservative amino acid modifications. The term “conservative modified variants” refers to polypeptides that can be encoded by nucleotide sequences having degenerate codon substitutions wherein at least one position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al., 1991; Ohtsuka et al., 1985; Rossolini et al., 1994). Additionally, one skilled in the art will recognize that individual substitutions, deletions, or additions to a nucleic acid, peptide, polypeptide, or polypeptide sequence that alters, adds, or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a “conservative modification” where the modification results in the substitution of an amino acid with a chemically similar amino acid. Conservative modified variants provide similar biological activity as the unmodified polypeptide. Conservative substitution tables listing functionally similar amino acids are known in the art. See Creighton, 1984.

The term “conservatively modified variant” also refers to a peptide having an amino acid residue sequence substantially identical to a sequence of a polypeptide of the presently disclosed subject matter in which one or more residues have been conservatively substituted with a functionally similar residue. Examples of conservative substitutions include the substitution of one non-polar (hydrophobic) residue such as isoleucine, valine, leucine or methionine for another; the substitution of one polar (hydrophilic) residue for another such as between arginine and lysine, between glutamine and asparagine, between glycine and serine; the substitution of one basic residue such as lysine, arginine or histidine for another; or the substitution of one acidic residue, such as aspartic acid or glutamic acid for another.

Amino acid substitutions, such as those which might be employed in modifying the polypeptides described herein, are generally based on the relative similarity of the amino acid side-chain substituents, for example, their hydrophobicity, hydrophilicity, charge, size, and the like. An analysis of the size, shape and type of the amino acid side-chain substituents reveals that arginine, lysine and histidine are all positively charged residues; that alanine, glycine and serine are all of similar size; and that phenylalanine, tryptophan and tyrosine all have a generally similar shape. Therefore, based upon these considerations, arginine, lysine and histidine; alanine, glycine and serine; and phenylalanine, tryptophan and tyrosine; are defined herein as biologically functional equivalents. Other biologically functionally equivalent changes will be appreciated by those of skill in the art.

In making biologically functional equivalent amino acid substitutions, the hydropathic index of amino acids can be considered. Each amino acid has been assigned a hydropathic index on the basis of their hydrophobicity and charge characteristics, these are: isoleucine (+4.5); valine (+4.2); leucine (+3.8); phenylalanine (+2.8); cysteine (+2.5); methionine (+1.9); alanine (+1.8); glycine (−0.4); threonine (−0.7); serine (−0.8); tryptophan (−0.9); tyrosine (−1.3); proline (−1.6); histidine (−3.2); glutamate (−3.5); glutamine (−3.5); aspartate (−3.5); asparagine (−3.5); lysine (−3.9); and arginine (4.5).

The importance of the hydropathic amino acid index in conferring interactive biological function on a protein is generally understood in the art (Kyte & Doolittle, 1982, incorporated herein by reference). It is known that certain amino acids can be substituted for other amino acids having a similar hydropathic index or score and still retain a similar biological activity. In making changes based upon the hydropathic index, substitutions of amino acids can involve amino acids for which the hydropathic indices are in some embodiments within ±2 of the original value, in some embodiments within ±1 of the original value, and in some embodiments within ±0.5 of the original value.

It is also understood in the art that the substitution of like amino acids can be made effectively on the basis of hydrophilicity. U.S. Pat. No. 4,554,101, incorporated herein by reference, states that the greatest local average hydrophilicity of a protein, as governed by the hydrophilicity of its adjacent amino acids, correlates with its immunogenicity and antigenicity, i.e. with a biological property of the protein. It is understood that an amino acid can be substituted for another having a similar hydrophilicity value and still obtain a biologically equivalent protein.

As detailed in U.S. Pat. No. 4,554,101, the following hydrophilicity values have been assigned to amino acid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0±1); glutamate (+3.0±1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0); threonine (−0.4); proline (−0.5±1); alanine (−0.5); histidine (−0.5); cysteine (−1.0); methionine (−1.3); valine (−1.5); leucine (−1.8); isoleucine (−1.8); tyrosine (−2.3); phenylalanine (−2.5); tryptophan (−3.4).

In making changes based upon similar hydrophilicity values, substitutions of amino acids can involve amino acids for which the hydrophilicity values are in some embodiments within ±2 of the original value, in some embodiments within ±1 of the original value, and in some embodiments within +0.5 of the original value.

While discussion has focused on functionally equivalent polypeptides arising from amino acid changes, it will be appreciated that these changes can be effected by alteration of the encoding DNA, taking into consideration also that the genetic code is degenerate and that two or more codons can code for the same amino acid.

In some embodiments, the sequence having substantial identity contains a deletion or insertion of at least one amino acid. In some embodiments, the deletion or insertion is of less than about ten amino acids. In some embodiments, the deletion or insertion is of less than about three amino acids.

In some embodiments, the sequence having substantial identity encodes a substitution in at least one amino acid.

Embodiments of the presently disclosed subject matter also provide an isolated polypeptide comprising a polypeptide sequence selected from the group consisting of:

-   -   (a) a polypeptide sequence having substantial identity to a         polypeptide sequence listed in SEQ ID NO: 2, or a domain or         feature thereof;     -   (b) a polypeptide sequence encoded by a nucleotide sequence         identical to or having substantial identity to a nucleotide         sequence that hybridizes under highly stringent conditions of         hybridization of 65° C. in 6×SSC, followed by a final washing         step of at least 15 minutes at 65° C. in 0.1×SSC to a nucleotide         sequence listed in SEQ ID NO: 1, or an exon, domain, or feature         thereof, or a sequence complementary thereto; and     -   (c) a functional fragment of (a) or (b).

In some embodiments, a polypeptide having substantial identity to a polypeptide sequence listed in SEQ ID NO: 2, or a domain or feature thereof, is an allelic variant of the polypeptide sequence listed in SEQ ID NO: 2. In some embodiments, a polypeptide having substantial identity to a polypeptide sequence listed in SEQ ID NO: 2, or a domain or feature thereof, is a naturally occurring variant of the polypeptide sequence listed in SEQ ID NO: 2. In some embodiments, a polypeptide having substantial identity to a polypeptide sequence listed in SEQ ID NO: 2, or a domain or feature thereof, is a polymorphic variant of the polypeptide sequence listed in SEQ ID NO: 2.

In some embodiments, the polypeptide is an ortholog of a polypeptide comprising the amino acid sequence listed in SEQ ID NO: 2. In some embodiments, the polypeptide is a functional fragment or domain of an ortholog of a polypeptide comprising the amino acid sequence listed in SEQ ID NOs: 2. In some embodiments, the polypeptide is a chimera, where the chimera comprises a functional polypeptide domain, including, but not limited to, a domain, a repeat, a post-translational modification site, and combinations thereof. In some embodiments, the polypeptide is a plant polypeptide. In some embodiments, the plant is a dicot. In some embodiments, the plant is a gymnosperm. In some embodiments, the plant is a monocot. In some embodiments, the monocot is a cereal. In some embodiments, the cereal can be, for example, maize, wheat, barley, oats, rye, millet, sorghum, triticale, secale, einkorn, spelt, emmer, teff, milo, flax, gramma grass, Tripsacum, or teosinte. In some embodiments, the cereal is maize.

In some embodiments, the polypeptide is expressed in a specific location or tissue of a plant. In some embodiments, the location or tissue includes, but is not limited to, epidermis, vascular tissue, meristem, cambium, cortex, or pith. In some embodiments, the location or tissue is leaf or sheath, root, flower, and developing ovule or seed. In some embodiments, the location or tissue can be, for example, epidermis, root, vascular tissue, meristem, cambium, cortex, pith, leaf, or flower. In some embodiments, the location or tissue is a seed.

In some embodiments, the polypeptide sequence is encoded by a nucleotide sequence that hybridizes under highly stringent conditions of hybridization of 65° C. in 6×SSC, followed by a final washing step of at least 15 minutes at 65° C. in 0.1×SSC to the nucleotide sequence of SEQ ID NO: 1, or a fragment, domain, or feature thereof or a sequence complementary thereto, wherein the nucleotide sequence includes a deletion or insertion of at least one nucleotide. In some embodiments, the deletion or insertion is of less than about thirty nucleotides. In some embodiments, the deletion or insertion is of less than about five nucleotides. In some embodiments, the polypeptide sequence encoded by a nucleotide sequence that hybridizes under highly stringent conditions of hybridization of 65° C. in 6×SSC, followed by a final washing step of at least 15 minutes at 65° C. in 0.1×SSC to the nucleotide sequence of SEQ ID NO: 1, or a fragment, domain, or feature thereof or a sequence complementary thereto, includes a substitution of at least one codon. In some embodiments, the substitution is conservative. In some embodiments, the polypeptide sequences having substantial identity to the polypeptide sequence of SEQ ID NO: 2, or a fragment, domain, repeat, feature, or chimera thereof, includes a deletion or insertion of at least one amino acid.

The polypeptides of the presently disclosed subject matter, fragments thereof, or variants thereof, can comprise any number of contiguous amino acid residues from a polypeptide of the presently disclosed subject matter, wherein the number of residues is selected from the group of integers consisting of from 10 to the number of residues in a full-length polypeptide of the presently disclosed subject matter. In some embodiments, the portion or fragment of the polypeptide is a functional polypeptide. The presently disclosed subject matter includes active polypeptides having specific activity of at least in some embodiments 20%, in some embodiments 30%, in some embodiments 40%, in some embodiments 50%, in some embodiments 60%, in some embodiments 70%, in some embodiments 80%, in some embodiments 90%, and in some embodiments 95% that of the native (non-synthetic) endogenous polypeptide. Further, the substrate specificity (k_(cat)/K_(m)) can be substantially identical to the native (non-synthetic), endogenous polypeptide. Typically the K_(m) will be at least in some embodiments 30%, in some embodiments 40%, in some embodiments 50% of the native, endogenous polypeptide; and in some embodiments at least 60%, in some embodiments 70%, in some embodiments 80%, and in some embodiments 90% of the native, endogenous polypeptide. Methods of assaying and quantifying measures of activity and substrate specificity are well known to those of skill in the art.

The isolated polypeptides of the presently disclosed subject matter can elicit production of an antibody specifically reactive to a polypeptide of the presently disclosed subject matter when presented as an immunogen. Therefore, the polypeptides of the presently disclosed subject matter can be employed as immunogens for constructing antibodies immunoreactive to a polypeptide of the presently disclosed subject matter for such purposes including, but not limited to, immunoassays or polypeptide purification techniques. Immunoassays for determining binding are well known to those of skill in the art and include, but are not limited to enzyme-linked immunosorbent assays (ELISA) and competitive immunoassays.

Embodiments of the presently disclosed subject matter also relate to chimeric polypeptides encoded by the isolated nucleic acid molecules of the present disclosure including a chimeric polypeptide containing a polypeptide sequence encoded by an isolated nucleic acid containing a nucleotide sequence selected from the group consisting of:

-   -   (a) a nucleotide sequence that hybridizes under highly stringent         conditions of hybridization of 65° C. in 6×SSC, followed by a         final washing step of at least 15 minutes at 65° C. in 0.1×SSC         to a nucleotide sequence listed in SEQ ID NO: 1, or an exon,         domain, or feature thereof;     -   (b) a nucleotide sequence complementary (for example, fully         complementary) to (a); and     -   (c) a nucleotide sequence which is the reverse complement (for         example, full reverse complement) of (a);     -   (d) or a functional fragment thereof.         IV. Controlling and Altering the Expression of Nucleic Acid         Molecules

IV.A. General Considerations

One aspect of the presently disclosed subject matter provides compositions and methods for altering (i.e. increasing or decreasing) the level of nucleic acid molecules and/or polypeptides of the presently disclosed subject matter in plants. In particular, the nucleic acid molecules and polypeptides of the presently disclosed subject matter are expressed constitutively, temporally, or spatially (e.g. at developmental stages), in certain tissues, and/or quantities, which are uncharacteristic of non-recombinantly engineered plants. Therefore, the presently disclosed subject matter provides utility in such exemplary applications as altering the specified characteristics identified above.

The isolated nucleic acid molecules of the presently disclosed subject matter are useful for expressing a polypeptide of the presently disclosed subject matter in a recombinantly engineered cell such as a bacterial, yeast, insect, mammalian, or plant cell. Expressing cells can produce the polypeptide in a non-natural condition (e.g. in quantity, composition, location, and/or time) because they have been genetically altered to do so. Those skilled in the art are knowledgeable in the numerous expression systems available for expression of nucleic acids encoding a polypeptide of the presently disclosed subject matter.

Embodiments of the presently disclosed subject matter provide an expression cassette comprising a promoter sequence operably linked to an isolated nucleic acid, the isolated nucleic acid comprising:

-   -   (a) a nucleotide sequence that hybridizes under highly stringent         conditions of hybridization of 65° C. in 6×SSC, followed by a         final washing step of at least 15 minutes at 65° C. in 0.1×SSC         to a nucleotide sequence listed in SEQ ID NO: 1, or a fragment,         domain, or feature thereof;     -   (b) a nucleotide sequence complementary (for example, fully         complementary) to (a); and     -   (c) a nucleotide sequence that is the reverse complement (for         example, the full reverse complement) of (a).

Further encompassed within the presently disclosed subject matter is a recombinant vector comprising an expression cassette according to the embodiments of the presently disclosed subject matter. Also encompassed are plant cells comprising expression cassettes according to the present disclosure, and plants comprising these plant cells. In some embodiments, the plant is a dicot. In some embodiments, the plant is a gymnosperm. In some embodiments, the plant is a monocot. In some embodiments, the monocot is a cereal. In some embodiments, the cereal is, for example, maize, wheat, barley, oats, rye, millet, sorghum, triticale, secale, einkorn, spelt, emmer, teff, milo, flax, gramma grass, Tripsacum or teosinte. In some embodiments, the cereal is maize.

In some embodiments, the expression cassette is expressed throughout the plant. In some embodiments, the expression cassette is expressed in a specific location or tissue of a plant. In some embodiments, the location or tissue includes, but is not limited to, epidermis, root, vascular tissue, meristem, cambium, cortex, pith, leaf, flower, seed, and combinations thereof. In some embodiments, the location or tissue is a seed. In some embodiments, the location or tissue is a protein body of a seed.

Embodiments of the presently disclosed subject matter also relate to an expression vector comprising a nucleic acid molecule selected from the group consisting of:

-   -   (a) a nucleic acid encoding a polypeptide as listed in SEQ ID         NO: 2, or ortholog thereof;     -   (b) a fragment, domain, or featured region of a nucleotide         sequence that hybridizes under highly stringent conditions of         hybridization of 65° C. in 6×SSC, followed by a final washing         step of at least 15 minutes at 65° C. in 0.1×SSC to a nucleotide         sequence listed in SEQ ID NO: 1; and     -   (c) a complete nucleotide sequence that hybridizes under highly         stringent conditions of hybridization of 65° C. in 6×SSC,         followed by a final washing step of at least 15 minutes at         65° C. in 0.1×SSC to a nucleotide sequence listed in SEQ ID NO:         1, or a fragment thereof, in combination with a heterologous         sequence.

In some embodiments, the expression vector comprises one or more elements including, but not limited to, a promoter-enhancer sequence, a selection marker sequence, an origin of replication, an epitope tag-encoding sequence, and an affinity purification tag-encoding sequence. In some embodiments, the promoter-enhancer sequence comprises, for example, the cauliflower mosaic virus (CaMV) 35S promoter, the CaMV 19S promoter, the tobacco PR-1a promoter, the ubiquitin promoter, or the phaseolin promoter. In some embodiments, the promoter is operable in plants, and in some embodiments, the promoter is a constitutive or inducible promoter. In some embodiments, the selection marker sequence encodes an antibiotic resistance gene. In some embodiments, the epitope tag sequence encodes the V5 epitope tag (GKPIPNPLLGLDST; SEQ ID NO: 9; Southern et al., 1991), the peptide FHHTT (SEQ ID NO: 10), hemaglutinin, or glutathione-5-transferase. In some embodiments the affinity purification tag sequence encodes a polyamino acid sequence or a polypeptide. In some embodiments, the polyamino acid sequence comprises polyhistidine. In some embodiments, the polypeptide is chitin-binding domain or glutathione-5-transferase. In some embodiments, the affinity purification tag sequence comprises an intein encoding sequence.

In some embodiments, the expression vector comprises a eukaryotic expression vector, and in some embodiments, the expression vector comprises a prokaryotic expression vector. In some embodiments, the eukaryotic expression vector comprises a tissue-specific promoter. In some embodiments, the expression vector is operable in plants.

Embodiments of the presently disclosed subject matter also relate to a cell comprising a nucleic acid construct comprising an expression vector and a nucleic acid comprising a nucleic acid encoding a polypeptide that is an ortholog of a polypeptide as listed in SEQ ID NO: 2, or a nucleotide sequence that hybridizes under highly stringent conditions of hybridization of 65° C. in 6×SSC, followed by a final washing step of at least 15 minutes at 65° C. in 0.1×SSC to a nucleotide sequence listed in SEQ ID NO: 1, or a subsequence thereof, in combination with a heterologous sequence.

In some embodiments, the cell is a bacterial cell, a fungal cell, a plant cell, or an animal cell. In some embodiments, the polypeptide is expressed in a specific location or tissue of a plant. In some embodiments, the location or tissue includes, but is not limited to, epidermis, root, vascular tissue, meristem, cambium, cortex, pith, leaf, flower, seed, and combinations thereof. In some embodiments, the location or tissue is a seed.

Prokaryotic cells including, but not limited to, Escherichia coli and other microbial strains known to those in the art, can be used a host cells. Methods for expressing polypeptides in prokaryotic cells are well known to those in the art and can be found in many laboratory manuals such as Sambrook & Russell, 2001. A variety of promoters, ribosome binding sites, and operators to control expression are available to those skilled in the art, as are selectable markers such as antibiotic resistance genes. The type of vector is chosen to allow for optimal growth and expression in the selected cell type.

A variety of eukaryotic expression systems are available such as, for example, yeast, insect cell lines, plant cells, and mammalian cells. Expression and synthesis of heterologous polypeptides in yeast is well known (see Sherman et al., 1982). Yeast strains widely used for production of eukaryotic polypeptides are Saccharomyces cerevisiae and Pichia pastoris, and vectors, strains, and protocols for expression are available from commercial suppliers (e.g., Invitrogen Corp., Carlsbad, Calif., United States of America).

Mammalian cell systems can be transformed with expression vectors for production of polypeptides. Suitable host cell lines available to those in the art include, but are not limited to, the HEK293, BHK21, and CHO cells lines. Expression vectors for these cells can include expression control sequences such as an origin of replication, a promoter, (e.g., the CMV promoter, a Herpes Simplex Virus thymidine kinase (HSV-tk) promoter or phosphoglycerate kinase (pgk) promoter), an enhancer, and polypeptide processing sites such as ribosome binding sites, RNA splice sites, polyadenylation sites, and transcription terminator sequences. Other animal cell lines useful for the production of polypeptides are available commercially or from depositories such as the American Type Culture Collection (Manassas, Va., United States of America).

Expression vectors for expressing polypeptides in insect cells are usually derived from baculovirus or other viruses known in the art. A number of suitable insect cell lines are available including, but not limited to, mosquito larvae, silkworm, armyworm (for example, Spodoptera frugiperda), moth, and Drosophila cell lines.

Methods of transforming animal and lower eukaryotic cells are known. Numerous methods can be used to introduce heterologous DNA into eukaryotic cells including, but not limited to, calcium phosphate precipitation, fusion of the recipient cell with bacterial protoplasts containing the DNA, treatment of the recipient cells with liposomes containing the DNA, DEAE dextran, electroporation, biolistics, and microinjection of the DNA directly into the cells. Transformed cells are cultured using means well known in the art (see Kuchler, 1997).

Once a polypeptide of the presently disclosed subject matter is expressed it can be isolated and purified from the expressing cells using methods known to those skilled in the art. The purification process can be monitored using Western blot techniques, radioimmunoassay, or other standard immunoassay techniques. Polypeptide purification techniques are commonly known and used by those skilled in the art (see Scopes, 1982; Deutscher, 1990).

Embodiments of the presently disclosed subject matter provide a method for producing a recombinant polypeptide in which the expression vector comprise one or more elements including, but not limited to, a promoter-enhancer sequence, a selection marker sequence, an origin of replication, an epitope tag-encoding sequence, and an affinity purification tag-encoding sequence. In some embodiments, the nucleic acid construct comprises an epitope tag-encoding sequence and the isolating step employs an antibody specific for the epitope tag. In some embodiments, the nucleic acid construct comprises a polyamino acid-encoding sequence and the isolating step employs a resin comprising a polyamino acid binding substance, in some embodiments where the polyamino acid is polyhistidine and the polyamino acid binding resin is nickel-charged agarose resin. In some embodiments, the nucleic acid construct comprises a polypeptide-encoding sequence and the isolating step employs a resin comprising a polypeptide binding substance. In some embodiments, the polypeptide is a chitin-binding domain and the resin contains chitin-sepharose.

The polypeptides of the presently disclosed subject matter can be synthesized using non-cellular synthetic methods known to those in the art. Techniques for solid phase synthesis are disclosed in Barany & Merrifield, 1980; Merrifield et al., 1963; Stewart & Young, 1984.

The presently disclosed subject matter further provides a method for modifying (i.e. increasing or decreasing) the concentration or composition of a polypeptide of the presently disclosed subject matter in a plant or part thereof. Modification can be effected by increasing or decreasing the concentration and/or the composition (i.e. the ration of the polypeptides of the presently disclosed subject matter) in a plant. The method comprises introducing into a plant cell an expression cassette comprising a nucleic acid molecule of the presently disclosed subject matter as disclosed above to obtain a transformed plant cell or tissue, and culturing the transformed plant cell or tissue. The nucleic acid molecule can be under the regulation of a constitutive or inducible promoter. The method can further comprise inducing or repressing expression of a nucleic acid molecule of a sequence in the plant for a time sufficient to modify the concentration and/or composition in the plant or plant part.

A plant or plant part having modified expression of a nucleic acid molecule of the presently disclosed subject matter can be analyzed and selected using methods known to those skilled in the art including, but not limited to, Southern blotting, DNA sequencing, or PCR analysis using primers specific to the nucleic acid molecule and detecting amplicons produced therefrom.

In general, a concentration or composition is increased or decreased by at least in some embodiments 5%, in some embodiments 10%, in some embodiments 20%, in some embodiments 30%, in some embodiments 40%, in some embodiments 50%, in some embodiments 60%, in some embodiments 70%, in some embodiments 80%, and in some embodiments 90% relative to a native control plant, plant part, or cell lacking the expression cassette.

IV.B. Homologous Recombination

In some embodiments, at least one genomic copy corresponding to a nucleotide sequence of the presently disclosed subject matter is modified in the genome of the plant by homologous recombination as further illustrated in Paszkowski et al., 1988. This technique uses the ability of homologous sequences to recognize each other and to exchange nucleotide sequences between respective nucleic acid molecules by a process known in the art as homologous recombination. Homologous recombination can occur between the chromosomal copy of a nucleotide sequence in a cell and an incoming copy of the nucleotide sequence introduced in the cell by transformation. Specific modifications are thus accurately introduced in the chromosomal copy of the nucleotide sequence. In some embodiments, the regulatory elements of the nucleotide sequence of the presently disclosed subject matter are modified. Such regulatory elements are easily obtainable by screening a genomic library using the nucleotide sequence of the presently disclosed subject matter, or a portion thereof, as a probe. The existing regulatory elements are replaced by different regulatory elements, thus altering expression of the nucleotide sequence, or they are mutated or deleted, thus abolishing the expression of the nucleotide sequence. In some embodiments, the nucleotide sequence is modified by deletion of a part of the nucleotide sequence or the entire nucleotide sequence, or by mutation. Expression of a mutated polypeptide in a plant cell is also provided in the presently disclosed subject matter. Recent refinements of this technique to disrupt endogenous plant genes have been disclosed (Kempin et al., 1997 and Miao & Lam, 1995).

In some embodiments, a mutation in the chromosomal copy of a nucleotide sequence is introduced by transforming a cell with a chimeric oligonucleotide composed of a contiguous stretch of RNA and DNA residues in a duplex conformation with double hairpin caps on the ends. An additional feature of the oligonucleotide is for example the presence of 2′-O-methylation at the RNA residues. The RNA/DNA sequence is designed to align with the sequence of a chromosomal copy of a nucleotide sequence of the presently disclosed subject matter and to contain the desired nucleotide change. For example, this technique is further illustrated in U.S. Pat. No. 5,501,967 and Zhu et al., 1999.

IV.C. Overexpression in a Plant Cell

In some embodiments, a nucleotide sequence of the presently disclosed subject matter encoding a polypeptide is over-expressed. Examples of nucleic acid molecules and expression cassettes for over-expression of a nucleic acid molecule of the presently disclosed subject matter are disclosed above. Methods known to those skilled in the art of over-expression of nucleic acid molecules are also encompassed by the presently disclosed subject matter.

In some embodiments, the expression of the nucleotide sequence of the presently disclosed subject matter is altered in every cell of a plant. This can be obtained, for example, though homologous recombination or by insertion into a chromosome. This can also be obtained, for example, by expressing a sense or antisense RNA, zinc finger polypeptide or ribozyme under the control of a promoter capable of expressing the sense or antisense RNA, zinc finger polypeptide, or ribozyme in every cell of a plant. Constitutive, inducible, tissue-specific, or developmentally-regulated expression are also within the scope of the presently disclosed subject matter and result in a constitutive, inducible, tissue-specific, or developmentally-regulated alteration of the expression of a nucleotide sequence of the presently disclosed subject matter in the plant cell. Constructs for expression of the sense or antisense RNA, zinc finger polypeptide, or ribozyme, or for over-expression of a nucleotide sequence of the presently disclosed subject matter, can be prepared and transformed into a plant cell according to the teachings of the presently disclosed subject matter, for example, as disclosed herein.

IV.D. Construction of Plant Expression Vectors

Coding sequences intended for expression in transgenic plants can be first assembled in expression cassettes operably linked to a suitable promoter expressible in plants. The expression cassettes can also comprise any further sequences required or selected for the expression of the transgene. Such sequences include, but are not limited to, transcription terminators, extraneous sequences to enhance expression such as introns, vital sequences, and sequences intended for the targeting of the gene product to specific organelles and cell compartments. These expression cassettes can then be easily transferred to the plant transformation vectors disclosed below. The following is a description of various components of typical expression cassettes.

IV.D.1. Promoters

The selection of the promoter used in expression cassettes can determine the spatial and temporal expression pattern of the transgene in the transgenic plant. Selected promoters can express transgenes in specific cell types (for example, leaf epidermal cells, mesophyll cells, root cortex cells, and/or endosperm cells) or in specific tissues or organs (for example, roots, leaves, flowers, and/or seeds) and the selection can reflect the desired location for accumulation of the gene product. Alternatively, the selected promoter can drive expression of the gene under various inducing conditions. Promoters vary in their strengths; i.e., their abilities to promote transcription. Depending upon the host cell system utilized, any one of a number of suitable promoters can be used, including the gene's native promoter. The following are non-limiting examples of promoters that can be used in expression cassettes.

IV.D.1.a. Constitutive Expression: the Ubiguitin Promoter

Ubiquitin is a gene product known to accumulate in many cell types and its promoter has been cloned from several species for use in transgenic plants (e.g. sunflower—Binet et al., 1991; maize—Christensen & Quail, 1989; and Arabidopsis—Callis et al., 1990; Norris et al., 1993). The maize ubiquitin promoter has been developed in transgenic monocot systems and its sequence and vectors constructed for monocot transformation are disclosed in the patent publication EP 0 342 926 (to Lubrizol) which is herein incorporated by reference. Taylor et al., 1993, describes a vector (pAHC25) that comprises the maize ubiquitin promoter and first intron and its high activity in cell suspensions of numerous monocotyledons when introduced via microprojectile bombardment. The Arabidopsis ubiquitin promoter is suitable for use with the nucleotide sequences of the presently disclosed subject matter. The ubiquitin promoter is suitable for gene expression in transgenic plants, both monocotyledons and dicotyledons. Suitable vectors are derivatives of pAHC25 or any of the transformation vectors disclosed herein, modified by the introduction of the appropriate ubiquitin promoter and/or intron sequences.

IV.D.1.b. Constitutive Expression: the CaMV 35S Promoter

Construction of the plasmid pCGN1761 is disclosed in the published patent application EP 0 392 225 (Example 23), which is hereby incorporated by reference. PCGN1761 contains the “double” CaMV 35S promoter and the tml transcriptional terminator with a unique EcoRI site between the promoter and the terminator and has a pUC-type backbone. A derivative of pCGN1761 is constructed which has a modified polylinker that includes Not[and XhoI sites in addition to the existing EcoRI site. This derivative is designated pCGN1761 ENX. pCGN1761ENX is useful for the cloning of cDNA sequences or coding sequences (including microbial ORF sequences) within its polylinker for the purpose of their expression under the control of the 35S promoter in transgenic plants. The entire 35S promoter-coding sequence-tml terminator cassette of such a construction can be excised by Hind III, Sph I, Sal I, and Xba I sites 5′ to the promoter and Xba I, BamH I and Bgl I sites 3′ to the terminator for transfer to transformation vectors such as those disclosed below. Furthermore, the double 35S promoter fragment can be removed by 5′ excision with Hind III, Sph I, Sal I, Xba I, or Pst I, and 3′ excision with any of the polylinker restriction sites (EcoR I, Not I or Xho I) for replacement with another promoter. If desired, modifications around the cloning sites can be made by the introduction of sequences that can enhance translation. This is particularly useful when overexpression is desired. For example, pCGN1761 ENX can be modified by optimization of the translational initiation site as disclosed in Example 37 of U.S. Pat. No. 5,639,949, incorporated herein by reference.

IV.D.1.c. Constitutive Expression: the Actin Promoter

Several isoforms of actin are known to be expressed in most cell types and consequently the actin promoter can be used as a constitutive promoter. In particular, the promoter from the rice Actl gene has been cloned and characterized (McElroy et al., 1990). A 1.3 kilobase (kb) fragment of the promoter was found to contain all the regulatory elements required for expression in rice protoplasts. Furthermore, numerous expression vectors based on the ActI promoter have been constructed specifically for use in monocotyledons (McElroy et al., 1991). These incorporate the Actl-intron 1, AdhI 5′ flanking sequence (from the maize alcohol dehydrogenase gene) and AdhI-intron 1 and sequence from the CaMV 35S promoter. Vectors showing highest expression were fusions of 35S and ActI intron or the Actl 5′ flanking sequence and the Actl intron. Optimization of sequences around the initiating ATG (of the β-glucuronidase (GUS) reporter gene) also enhanced expression. The promoter expression cassettes disclosed in McElroy et al., 1991, can be easily modified for gene expression and are particularly suitable for use in monocotyledonous hosts. For example, promoter-containing fragments are removed from the McElroy constructions and used to replace the double 35S promoter in PCGN 1761 ENX, which is then available for the insertion of specific gene sequences. The fusion genes thus constructed can then be transferred to appropriate transformation vectors. In a separate report, the rice Actl promoter with its first intron has also been found to direct high expression in cultured barley cells (Chibbar et al., 1993).

IV.D.1.d. Inducible Expression: PR-1 Promoters

The double 35S promoter in pCGN1761 ENX can be replaced with any other promoter of choice that will result in suitably high expression levels. By way of example, one of the chemically regulatable promoters disclosed in U.S. Pat. No. 5,614,395, such as the tobacco PR-1a promoter, can replace the double 35S promoter. Alternately, the Arabidopsis PR-1 promoter disclosed in Lebel et al., 1998, can be used. The promoter of choice can be excised from its source by restriction enzymes, but can alternatively be PCR-amplified using primers that carry appropriate terminal restriction sites. Should PCR-amplification be undertaken, the promoter can be re-sequenced to check for amplification errors after the cloning of the amplified promoter in the target vector. The chemically/pathogen regulatable tobacco PR-1a promoter is cleaved from plasmid pCIB1004 (for construction, see example 21 of EP 0 332 104, which is hereby incorporated by reference) and transferred to plasmid pCGN1761 ENX (Uknes et al., 1992). pCIB1004 is cleaved with Nco I and the resulting 3′ overhang of the linearized fragment is rendered blunt by treatment with T4 DNA polymerase. The fragment is then cleaved with Hind III and the resultant PR-1a promoter-containing fragment is gel purified and cloned into pCGN1761ENX from which the double 35S promoter has been removed. This is accomplished by cleavage with Xho I and blunting with T4 polymerase, followed by cleavage with Hind III, and isolation of the larger vector-terminator containing fragment into which the pCIB1004 promoter fragment is cloned. This generates a pCGN1761 ENX derivative with the PR-1 a promoter and the tml terminator and an intervening polylinkerwith unique EcoR I and Not I sites. The selected coding sequence can be inserted into this vector, and the fusion products (i.e. promoter-gene-terminator) can subsequently be transferred to any selected transformation vector, including those disclosed herein. Various chemical regulators can be employed to induce expression of the selected coding sequence in the plants transformed according to the presently disclosed subject matter, including the benzothiadiazole, isonicotinic acid, and salicylic acid compounds disclosed in U.S. Pat. Nos. 5,523,311 and 5,614,395.

IV.D.1.e. Inducible Expression: an Ethanol-Inducible Promoter

A promoter inducible by certain alcohols or ketones, such as ethanol, can also be used to confer inducible expression of a coding sequence of the presently disclosed subject matter. Such a promoter is for example the alcA gene promoter from Aspergillus nidulans (Caddick et al., 1998). In A. nidulans, the alcA gene encodes alcohol dehydrogenase 1, the expression of which is regulated by the AlcR transcription factors in presence of the chemical inducer. For the purposes of the presently disclosed subject matter, the CAT coding sequences in plasmid palcA:CAT comprising a alcA gene promoter sequence fused to a minimal 35S promoter (Caddick et al., 1998) are replaced by a coding sequence of the presently disclosed subject matter to form an expression cassette having the coding sequence under the control of the alcA gene promoter. This is carried out using methods known in the art.

IV.D.1.f. Inducible Expression: a Glucocorticoid-Inducible Promoter

Induction of expression of a nucleotide sequence of the presently disclosed subject matter using systems based on steroid hormones is also provided. For example, a glucocorticoid-mediated induction system is used (Aoyama & Chua, 1997) and gene expression is induced by application of a glucocorticoid, for example a synthetic glucocorticoid, for example dexamethasone, at a concentration ranging in some embodiments from 0.1 mM to 1 mM, and in some embodiments from 10 mM to 100 mM. For the purposes of the presently disclosed subject matter, the luciferase gene sequences Aoyama & Chua, 1997 are replaced by a nucleotide sequence of the presently disclosed subject matterto form an expression cassette having a nucleotide sequence of the presently disclosed subject matter under the control of six copies of the GAL4 upstream activating sequences fused to the 35S minimal promoter. This is carried out using methods known in the art. The trans-acting factor comprises the GAL4 DNA-binding domain (Keegan et al., 1986) fused to the transactivating domain of the herpes viral polypeptide VP16 (Triezenberg et al., 1988) fused to the hormone-binding domain of the rat glucocorticoid receptor (Picard et al., 1988). The expression of the fusion polypeptide is controlled either by a promoter known in the art or disclosed herein. A plant comprising an expression cassette comprising a nucleotide sequence of the presently disclosed subject matter fused to the 6×GAL4/minimal promoter is also provided. Thus, tissue- or organ-specificity of the fusion polypeptide is achieved leading to inducible tissue- or organ-specificity of the nucleotide sequence to be expressed.

IV.D.1.g. Root Specific Expression

Another pattern of gene expression is root expression. A suitable root promoter is the promoter of the maize metallothionein-like (MTL) gene disclosed in de Framond, 1991, and also in U.S. Pat. No. 5,466,785, each of which is incorporated herein by reference. This “MTL” promoter is transferred to a suitable vector such as pCGN1761 ENX for the insertion of a selected gene and subsequent transfer of the entire promoter-gene-terminator cassette to a transformation vector of interest.

IV.D.1.h. Wound-Inducible Promoters

Wound-inducible promoters can also be suitable for gene expression. Numerous such promoters have been disclosed (e.g. Xu et al., 1993; Logemann et al., 1989; Rohrmeier & Lehle, 1993; Firek et al., 1993; Warner et al., 1993) and all are suitable for use with the presently disclosed subject matter. Logemann et al., describe the 5′ upstream sequences of the dicotyledonous potato wunl gene. Xu et al. show that a wound-inducible promoter from the dicotyledon potato (pin2) is active in the monocotyledon rice. Further, Rohrmeier & Lehle describe the cloning of the maize Wipl cDNA that is wound induced and which can be used to isolate the cognate promoter using standard techniques. Similarly, Firek et al. and Warner et al. have disclosed a wound-induced gene from the monocotyledon Asparagus officinalis, which is expressed at local wound and pathogen invasion sites. Using cloning techniques well known in the art, these promoters can be transferred to suitable vectors, fused to the genes pertaining to the presently disclosed subject matter, and used to express these genes at the sites of plant wounding.

IV.D.1.i. Pith-Preferred Expression

PCT International Publication WO 93/07278, which is herein incorporated by reference, describes the isolation of the maize trpA gene, which is preferentially expressed in pith cells. The gene sequence and promoter extending up to −1726 basepairs (bp) from the start of transcription are presented. Using standard molecular biological techniques, this promoter, or parts thereof, can be transferred to a vector such as pCGN1761 where it can replace the 35S promoter and be used to drive the expression of a foreign gene in a pith-preferred manner. In fact, fragments containing the pith-preferred promoter or parts thereof can be transferred to any vector and modified for utility in transgenic plants.

IV.D.1.i. Leaf-Specific Expression

A maize gene encoding phosphoenol carboxylase (PEPC) has been disclosed by Hudspeth & Grula, 1989. Using standard molecular biological techniques, the promoter for this gene can be used to drive the expression of any gene in a leaf-specific manner in transgenic plants.

IV.D.1.k. Pollen-Specific Expression

WO 93/07278 describes the isolation of the maize calcium-dependent protein kinase (CDPK) gene that is expressed in pollen cells. The gene sequence and promoter extend up to 1400 basepairs (bp) from the start of transcription. Using standard molecular biological techniques, this promoter or parts thereof can be transferred to a vector such as pCGN1761 where it can replace the 35S promoter and be used to drive the expression of a nucleotide sequence of the presently disclosed subject matter in a pollen-specific manner.

IV.D.1.1. Seed-Specific Expression

In some embodiments, nucleic acid molecules of the presently disclosed subject matter can be expressed in the seed, and/or in a protein body present within a seed. As disclosed herein, a nucleotide sequence isolated from the Q protein gene, SEQ ID NO: 6, can be used to direct expression of heterologous sequences in the seeds of plants. Using standard molecular biological techniques, this promoter or parts thereof can be transferred to a vector such as pCGN1761 where it can replace the 35S promoter and be used to drive the expression of a nucleotide sequence of the presently disclosed subject matter in a seed-specific manner.

IV.D.2. Transcriptional Terminators

A variety of transcriptional terminators are available for use in expression cassettes. These are responsible for termination of transcription and correct mRNA polyadenylation. Appropriate transcriptional terminators are those that are known to function in plants and include the CaMV 35S terminator, the tml terminator, the nopaline synthase terminator, and the pea rbcS E9 terminator. These can be used in both monocotyledons and dicotyledons. In addition, a gene's native transcription terminator can be used.

IV.D.3. Sequences for the Enhancement or Regulation of Expression

Numerous sequences have been found to enhance gene expression from within the transcriptional unit and these sequences can be used in conjunction with the genes of the presently disclosed subject matter to increase their expression in transgenic plants.

Various intron sequences have been shown to enhance expression, particularly in monocotyledonous cells. For example, the introns of the maize AdhI gene have been found to significantly enhance the expression of the wild-type gene under its cognate promoter when introduced into maize cells. Intron 1 was found to be particularly effective and enhanced expression in fusion constructs with the chloramphenicol acetyltransferase gene (Callis et al., 1987). In the same experimental system, the intron from the maize bronze1 gene had a similar effect in enhancing expression. Intron sequences have been routinely incorporated into plant transformation vectors, typically within the non-translated leader.

A number of non-translated leader sequences derived from viruses are also known to enhance expression, and these are particularly effective in dicotyledonous cells. Specifically, leader sequences from Tobacco Mosaic Virus (TMV; the “W-sequence”), Maize Chlorotic Mottle Virus (MCMV), and Alfalfa Mosaic Virus (AMV) have been shown to be effective in enhancing expression (see e.g. Gallie et al., 1987; Skuzeski et al., 1990). Other leader sequences known in the art include, but are not limited to, picornavirus leaders, for example, encephalomyocarditis virus (EMCV) leader (5′ noncoding region; see Elroy-Stein et al., 1989); potyvirus leaders, for example, from Tobacco Etch Virus (TEV; see Allison et al., 1986); Maize Dwarf Mosaic Virus (MDMV; see Kong & Steinbiss 1998); human immunoglobulin heavy-chain binding polypeptide (BiP) leader (Macejak & Sarnow, 1991); untranslated leader from the coat polypeptide mRNA of alfalfa mosaic virus (AMV; RNA 4; see Jobling & Gehrke, 1987); tobacco mosaic virus (TMV) leader (Gallie et al., 1989); and Maize Chlorotic Mottle Virus (MCMV) leader (Lommel et al., 1991). See also, Della-Cioppa et al., 1987.

In addition to incorporating one or more of the aforementioned elements into the 5′ regulatory region of a target expression cassette of the presently disclosed subject matter, other elements can also be incorporated. Such elements include, but are not limited to, a minimal promoter. By minimal promoter it is intended that the basal promoter elements are inactive or nearly so in the absence of upstream or downstream activation. Such a promoter has low background activity in plants when there is no transactivator present or when enhancer or response element binding sites are absent. One minimal promoter that is particularly useful for target genes in plants is the Bz1 minimal promoter, which is obtained from the bronze1 gene of maize. The Bz1 core promoter is obtained from the “myc” mutant Bz1-luciferase construct pBz1 LucR98 via cleavage at the NheI site located at positions −53 to −58 (Roth et al., 1991). The derived Bz1 core promoter fragment thus extends from positions −53 to +227 and includes the Bz1 intron-1 in the 5′ untranslated region. Also useful for the presently disclosed subject matter is a minimal promoter created by use of a synthetic TATA element. The TATA element allows recognition of the promoter by RNA polymerase factors and confers a basal level of gene expression in the absence of activation (see generally, Mukumoto et al., 1993; Green, 2000.

IV.D.4. Targeting of the Gene Product Within the Cell

Various mechanisms for targeting gene products are known to exist in plants and the sequences controlling the functioning of these mechanisms have been characterized in some detail. For example, the targeting of gene products to the chloroplast is controlled by a signal sequence found at the amino terminal end of various polypeptides that is cleaved during chloroplast import to yield the mature polypeptides (see e.g., Comai et al., 1988). These signal sequences can be fused to heterologous gene products to affect the import of heterologous products into the chloroplast (Van den Broeck et al., 1985). DNA encoding for appropriate signal sequences can be isolated from the 5′ end of the cDNAs encoding the ribulose-1,5-bisphosphate carboxylase/oxygenase (RUBISCO) polypeptide, the chlorophyll a/b binding (CAB) polypeptide, the 5-enol-pyruvyl shikimate-3-phosphate (EPSP) synthase enzyme, the GS2 polypeptide and many other polypeptides which are known to be chloroplast localized. See also, the section entitled “Expression With Chloroplast Targeting” in Example 37 of U.S. Pat. No. 5,639,949, herein incorporated by reference.

Other gene products can be localized to other organelles such as the mitochondrion and the peroxisome (e.g. Unger et al., 1989). The cDNAs encoding these products can also be manipulated to effect the targeting of heterologous gene products to these organelles. Examples of such sequences are the nuclear-encoded ATPases and specific aspartate amino transferase isoforms for mitochondria. Targeting cellular polypeptide bodies has been disclosed by Rogers et al., 1985.

In addition, sequences have been characterized that control the targeting of gene products to other cell compartments. Amino terminal sequences are responsible for targeting to the endoplasmic reticulum (ER), the apoplast, and extracellular secretion from aleurone cells (Koehler & Ho, 1990). Additionally, amino terminal sequences in conjunction with carboxy terminal sequences are responsible for vacuolar targeting of gene products (Shinshi et al., 1990).

By the fusion of the appropriate targeting sequences disclosed above to transgene sequences of interest it is possible to direct the transgene product to any organelle or cell compartment. For chloroplast targeting, for example, the chloroplast signal sequence from the RUBISCO gene, the CAB gene, the EPSP synthase gene, or the GS2 gene is fused in frame to the amino terminal ATG of the transgene. The signal sequence selected can include the known cleavage site, and the fusion constructed can take into account any amino acids after the cleavage site that are required for cleavage. In some cases this requirement can be fulfilled by the addition of a small number of amino acids between the cleavage site and the transgene ATG or, alternatively, replacement of some amino acids within the transgene sequence. Fusions constructed for chloroplast import can be tested for efficacy of chloroplast uptake by in vitro translation of in vitro transcribed constructions followed by in vitro chloroplast uptake using techniques disclosed by Bartlett et al., 1982 and Wasmann et al., 1986. These construction techniques are well known in the art and are equally applicable to mitochondria and peroxisomes.

And finally, using a nucleotide sequence comprising the Q protein promoter (SEQ ID NO: 6), seed-specific expression of a heterologous sequence can be accomplished. Thus, an expression construct comprising a heterologous coding sequence operably linked to SEQ ID NO: 6 can be employed to direct expression of the nucleotide sequence in the seed, and in some embodiments, can be used to produce protein bodies comprising the polypeptide encoded by the heterologous coding sequence.

The above-disclosed mechanisms for cellular targeting can be utilized not only in conjunction with their cognate promoters, but also in conjunction with heterologous promoters so as to effect a specific cell-targeting goal under the transcriptional regulation of a promoter that has an expression pattern different from that of the promoter from which the targeting signal derives.

IV.E. Construction of Plant Transformation Vectors

Numerous transformation vectors available for plant transformation are known to those of ordinary skill in the plant transformation art, and the genes pertinent to the presently disclosed subject matter can be used in conjunction with any such vectors. The selection of vector will depend upon the selected transformation technique and the target species for transformation. For certain target species, different antibiotic or herbicide selection markers might be employed. Selection markers used routinely in transformation include the nptII gene, which confers resistance to kanamycin and related antibiotics (Messing & Vieira, 1982; Bevan et al., 1983); the bargene, which confers resistance to the herbicide phosphinothricin (White et al., 1990; Spencer et al., 1990); the hph gene, which confers resistance to the antibiotic hygromycin (Blochinger & Diggelmann, 1984); the dhfr gene, which confers resistance to methotrexate (Bourouis & Jarry, 1983); the EPSP synthase gene, which confers resistance to glyphosate (U.S. Pat. Nos. 4,940,935 and 5,188,642); and the mannose-6-phosphate isomerase gene, which provides the ability to metabolize mannose (U.S. Pat. Nos. 5,767,378 and 5,994,629).

IV.E.1. Vectors Suitable for Agrobacterium Transformation

Many vectors are available for transformation using Agrobacterium tumefaciens. These typically carry at least one T-DNA border sequence and include vectors such as pBIN19 (Bevan, 1984). Below, the construction of two typical vectors suitable for Agrobacterium transformation is disclosed.

IV.E.1.a. PCIB200 and PCIB2001

The binary vectors pCIB200 and pCIB2001 are used for the construction of recombinant vectors for use with Agrobacterium and are constructed in the following manner. pTJS75kan is created by Nar I digestion of pTJS75 (Schmidhauser & Helinski, 1985) allowing excision of the tetracycline-resistance gene, followed by insertion of an Acc I fragment from pUC4K carrying an NPTII sequence (Messing & Vieira, 1982: Bevan et al., 1983: McBride & Summerfelt. 1990). Xho I linkers are ligated to the EcoRV fragment of PCIB7 which contains the left and right T-DNA borders, a plant selectable nos/nptil chimeric gene and the pUC polylinker (Rothstein et al., 1987), and the Xho 1-digested fragment are cloned into Sal 1-digested pTJS75kan to create pCIB200 (see also EP 0 332 104, example 19). pCIB200 contains the following unique polylinker restriction sites: EcoR I, Sst I, Kpn 1, Bgl II, Xba I, and Sal I. pCIB2001 is a derivative of pCIB200 created by the insertion into the polylinker of additional restriction sites. Unique restriction sites in the polylinker of pCIB2001 are EcoR I, Sst I, Kpn 1, Bgl II, Xba I, Sal I, Mlu I, Bcl I, Avr II, Apa I, Hpa I, and Stu I. pCIB2001, in addition to containing these unique restriction sites, also has plant and bacterial kanamycin selection, left and right T-DNA borders for Agrobacterium-mediated transformation, the RK2-derived trfA function for mobilization between E. coli and other hosts, and the OriT and OriV functions also from RK2. The pCIB2001 polylinker is suitable for the cloning of plant expression cassettes containing their own regulatory signals.

IV.E.1.b. pCIB10 and Hygromycin Selection Derivatives Thereof

The binary vector pCIB10 contains a gene encoding kanamycin resistance for selection in plants, T-DNA right and left border sequences, and incorporates sequences from the wide host-range plasmid pRK252 allowing it to replicate in both E. coli and Agrobacterium. Its construction is disclosed by Rothstein et al., 1987. Various derivatives of pCIB10 can be constructed which incorporate the gene for hygromycin B phosphotransferase disclosed by Gritz & Davies, 1983. These derivatives enable selection of transgenic plant cells on hygromycin only (pCIB743), or hygromycin and kanamycin (pCIB715, pCIB717).

IV.E.2. Vectors Suitable for non-Argrobacterium Transformation

Transformation without the use of Agrobacterium tumefaciens circumvents the requirement for T-DNA sequences in the chosen transformation vector, and consequently vectors lacking these sequences can be utilized in addition to vectors such as the ones disclosed above that contain T-DNA sequences. Transformation techniques that do not rely on Agrobacterium include transformation via particle bombardment, protoplast uptake (e.g. polyethylene glycol (PEG) and electroporation), and microinjection. The choice of vector depends largely on the species being transformed. Below, the construction of typical vectors suitable for non-Agrobacterium transformation is disclosed.

IV.E.2.a. PCIB3064

pCIB3064 is a pUC-derived vector suitable for direct gene transfer techniques in combination with selection by the herbicide BASTA® (glufosinate ammonium or phosphinothricin). The plasmid pCIB246 comprises the CaMV 35S promoter in operational fusion to the E. coli β-glucuronidase (GUS) gene and the CaMV 35S transcriptional terminator and is disclosed in the PCT International Publication WO 93/07278. The 35S promoter of this vector contains two ATG sequences 5′ of the start site. These sites are mutated using standard PCR techniques in such a way as to remove the ATGs and generate the restriction sites Ssp I and Pvu II. The new restriction sites are 96 and 37 bp away from the unique Sal I site and 101 and 42 bp away from the actual start site. The resultant derivative of pCIB246 is designated pCIB3025. The GUS gene is then excised from pCIB3025 by digestion with Sal I and Sac 1, the termini rendered blunt and religated to generate plasmid pCIB3060. The plasmid pJIT82 is obtained from the John Innes Centre, Norwich, England, and the 400 bp Sma I fragment containing the bar gene from Streptomyces viridochromogenes is excised and inserted into the Hpa I site of pCIB3060 (Thompson et al., 1987). This generated pCIB3064, which comprises the bar gene under the control of the CaMV 35S promoter and terminator for herbicide selection, a gene for ampicillin resistance (for selection in E. coli) and a polylinkerwith the unique sites Sph I, Pst I, Hind III, and BamH I. This vector is suitable for the cloning of plant expression cassettes containing their own regulatory signals.

IV.E.2.b. DSOG19 and DSOG35

pSOG35 is a transformation vector that utilizes the E. coli dihydrofolate reductase (DHFR) gene as a selectable marker conferring resistance to methotrexate. PCR is used to amplify the 35S promoter (−800 bp), intron 6 from the maize AdhI gene (−550 bp), and 18 bp of the GUS untranslated leader sequence from pSOG 10. A 250-bp fragment encoding the E. colidihydrofolate reductase type 11 gene is also amplified by PCR and these two PCR fragments are assembled with a Sac I-Pst I fragment from pB1221 (BD Biosciences Clontech, Palo Alto, Calif., United States of America) that comprises the pUC19 vector backbone and the nopaline synthase terminator. Assembly of these fragments generates pSOG19 that contains the 35S promoter in fusion with the intron 6 sequence, the GUS leader, the DHFR gene, and the nopaline synthase terminator. Replacement of the GUS leader in pSOG19 with the leader sequence from Maize Chlorotic Mottle Virus (MCMV) generates the vector pSOG35. pSOG19 and pSOG35 carry the pUC gene for ampicillin resistance and have Hind III, Sph I, Pst I, and EcoR I sites available for the cloning of foreign substances.

IV.E.3. Vector Suitable for Chloroplast Transformation

For expression of a nucleotide sequence of the presently disclosed subject matter in plant plastids, plastid transformation vector pPH143 (PCT International Publication WO 97/32011, example 36) is used. The nucleotide sequence is inserted into pPH143 thereby replacing the protoporphyrinogen oxidase (Protox) coding sequence. This vector is then used for plastid transformation and selection of transformants for spectinomycin resistance. Alternatively, the nucleotide sequence is inserted in pPH 143 so that it replaces the aadH gene. In this case, transformants are selected for resistance to Protox inhibitors.

IV.F. Transformation

Once a nucleotide sequence of the presently disclosed subject matter has been cloned into an expression system, it is transformed into a plant cell. The receptor and target expression cassettes of the presently disclosed subject matter can be introduced into the plant cell in a number of art-recognized ways. Methods for regeneration of plants are also well known in the art. For example, Ti plasmid vectors have been utilized for the delivery of foreign DNA, as well as direct DNA uptake, liposomes, electroporation, microinjection, and microprojectiles. In addition, bacteria from the genus Agrobacterium can be utilized to transform plant cells. Below are descriptions of representative techniques for transforming both dicotyledonous and monocotyledonous plants, as well as a representative plastid transformation technique.

IV.F.1. Transformation of Dicotyledons

Transformation techniques for dicotyledons are well known in the art and include Agrobacterium-based techniques and techniques that do not require Agrobacterium. Non-Agrobacterium techniques involve the uptake of heterologous genetic material directly by protoplasts or cells. This can be accomplished by PEG or electroporation-mediated uptake, particle bombardment-mediated delivery, or microinjection. Examples of these techniques are disclosed in Paszkowski et al., 1984; Potrykus et al., 1985; Reich et al., 1986; and Klein et al., 1987. In each case the transformed cells are regenerated to whole plants using standard techniques known in the art.

Agrobacterium-mediated transformation is a useful technique for transformation of dicotyledons because of its high efficiency of transformation and its broad utility with many different species. Agrobacterium transformation typically involves the transfer of the binary vector carrying the foreign DNA of interest (e.g. pCIB200 or pCIB2001) to an appropriate Agrobacterium strain which can depend on the complement of vir genes carried by the host Agrobacterium strain either on a co-resident Ti plasmid or chromosomally (e.g. strain CIB542 for pCIB200 and pCIB2001 (Uknes et al., 1993). The transfer of the recombinant binary vector to Agrobacterium is accomplished by a triparental mating procedure using E. coli carrying the recombinant binary vector, a helper E. coli strain that carries a plasmid such as pRK2013 and which is able to mobilize the recombinant binary vector to the target Agrobacterium strain. Alternatively, the recombinant binary vector can be transferred to Agrobacterium by DNA transformation (Hofgen & Willmitzer, 1988).

Transformation of the target plant species by recombinant Agrobacterium usually involves co-cultivation of the Agrobacterium with explants from the plant and follows protocols well known in the art. Transformed tissue is regenerated on selectable medium carrying the antibiotic or herbicide resistance marker present between the binary plasmid T-DNA borders.

Another approach to transforming plant cells with a gene involves propelling inert or biologically active particles at plant tissues and cells. This technique is disclosed in U.S. Pat. Nos. 4,945,050; 5,036,006; and 5,100,792; all to Sanford et al. Generally, this procedure involves propelling inert or biologically active particles at the cells under conditions effective to penetrate the outer surface of the cell and afford incorporation within the interior thereof. When inert particles are utilized, the vector can be introduced into the cell by coating the particles with the vector containing the desired gene. Alternatively, the target cell can be surrounded by the vector so that the vector is carried into the cell by the wake of the particle. Biologically active particles (e.g., dried yeast cells, dried bacterium, or a bacteriophage, each containing DNA sought to be introduced) can also be propelled into plant cell tissue.

IV.F.2. Transformation of Monocotyledons

Transformation of most monocotyledon species has now also become routine. Exemplary techniques include direct gene transfer into protoplasts using PEG or electroporation, and particle bombardment into callus tissue. Transformations can be undertaken with a single DNA species or multiple DNA species (i.e. co-transformation), and both these techniques are suitable for use with the presently disclosed subject matter. Co-transformation can have the advantage of avoiding complete vector construction and of generating transgenic plants with unlinked loci for the gene of interest and the selectable marker, enabling the removal of the selectable marker in subsequent generations, should this be regarded as desirable. However, a disadvantage of the use of co-transformation is the less than 100% frequency with which separate DNA species are integrated into the genome (Schocher et al., 1986).

Patent Applications EP 0 292 435, EP 0 392 225, and WO 93/07278 describe techniques for the preparation of callus and protoplasts from an elite inbred line of maize, transformation of protoplasts using PEG or electroporation, and the regeneration of maize plants from transformed protoplasts. Gordon-Kamm et al., 1990 and Fromm et al., 1990 have published techniques for transformation of A188-derived maize line using particle bombardment. Furthermore, WO 93/07278 and Koziel et al., 1993 describe techniques for the transformation of elite inbred lines of maize by particle bombardment. This technique utilizes immature maize embryos of 1.5-2.5 mm length excised from a maize ear 14-15 days after pollination and a PDS-1000/He Biolistic particle delivery device (Bio-Rad Laboratories, Hercules, Calif., United States of America) for bombardment.

Transformation of rice can also be undertaken by direct gene transfer techniques utilizing protoplasts or particle bombardment. Protoplast-mediated transformation has been disclosed for Japonica-types and Indica-types (Zhang et al., 1988; Shimamoto et al., 1989; Datta et al., 1990) of rice. Both types are also routinely transformable using particle bombardment (Christou et al., 1991). Furthermore, WO 93/21335 describes techniques for the transformation of rice via electroporation. Casas et al., 1993 discloses the production of transgenic sorghum plants by microprojectile bombardment.

European Patent Application EP 0 332 581 describes techniques for the generation, transformation, and regeneration of Pooideae protoplasts. These techniques allow the transformation of Dactylis and wheat. Furthermore, wheat transformation has been disclosed in Vasil et al., 1992 using particle bombardment into cells of type C long-term regenerable callus, and also by Vasil et al., 1993 and Weeks et al., 1993 using particle bombardment of immature embryos and immature embryo-derived callus.

A representative technique for wheat transformation, however, involves the transformation of wheat by particle bombardment of immature embryos and includes either a high sucrose or a high maltose step prior to gene delivery. Prior to bombardment, embryos (0.75-1 mm in length) are plated onto MS medium with 3% sucrose (Murashige & Skoog, 1962) and 3 mg/l 2,4-dichlorophenoxyacetic acid (2,4-D) for induction of somatic embryos, which is allowed to proceed in the dark. On the chosen day of bombardment, embryos are removed from the induction medium and placed onto the osmoticum (i.e. induction medium with sucrose or maltose added at the desired concentration, typically 15%). The embryos are allowed to plasmolyze for 2-3 hours and are then bombarded. Twenty embryos per target plate are typical, although not critical. An appropriate gene-carrying plasmid (such as pCIB3064 or pSG35) is precipitated onto micrometer size gold particles using standard procedures. Each plate of embryos is shot with biolistics device using a burst pressure of about 1000 pounds per square inch (psi) using a standard 80 mesh screen. After bombardment, the embryos are placed back into the dark to recover for about 24 hours (still on osmoticum). After 24 hours, the embryos are removed from the osmoticum and placed back onto induction medium where they stay for about a month before regeneration. Approximately one month later the embryo explants with developing embryogenic callus are transferred to regeneration medium (MS+1 mg/liter NM, 5 mg/liter GA), further containing the appropriate selection agent (10 mg/l BASTA® in the case of pCIB3064 and 2 mg/l methotrexate in the case of pSOG35). After approximately one month, developed shoots are transferred to larger sterile containers known as “GA7s” which contain half-strength MS, 2% sucrose, and the same concentration of selection agent.

Transformation of monocotyledons using Agrobacterium has also been disclosed. See WO 94/00977 and U.S. Pat. No. 5,591,616, both of which are incorporated herein by reference. See also Negrotto et al., 2000, incorporated herein by reference. Zhao et al., 2000 specifically discloses transformation of sorghum with Agrobacterium. See also U.S. Pat. No. 6,369,298.

Rice (Oryza sativa) can be used for generating transgenic plants. Various rice cultivars can be used (Hiei et al., 1994; Dong et al., 1996; Hiei et al., 1997). Also, the various media constituents disclosed below can be either varied in quantity or substituted. Embryogenic responses are initiated and/or cultures are established from mature embryos by culturing on MS-CIM medium (MS basal salts, 4.3 g/liter; B5 vitamins (200×), 5 ml/liter; sucrose, 30 g/liter; proline, 500 mg/liter; glutamine, 500 mg/liter; casein hydrolysate, 300 mg/liter; 2,4-D (1 mg/ml), 2 ml/liter; pH adjusted to 5.8 with 1 N KOH; Phytagel, 3 g/liter). Either mature embryos at the initial stages of culture response or established culture lines are inoculated and co-cultivated with the Agrobacterium tumefaciens strain LBA4404 (Agrobacterium) containing the desired vector construction. Agrobacterium is cultured from glycerol stocks on solid YPC medium (plus 100 mg/L spectinomycin and any other appropriate antibiotic) for about 2 days at 28° C. Agrobacterium is re-suspended in liquid MS-CIM medium. The Agrobacterium culture is diluted to an OD₆₀₀ of 0.2-0.3 and acetosyringone is added to a final concentration of 200 μM. Acetosyringone is added before mixing the solution with the rice cultures to induce Agrobacterium for DNA transfer to the plant cells. For inoculation, the plant cultures are immersed in the bacterial suspension. The liquid bacterial suspension is removed and the inoculated cultures are placed on co-cultivation medium and incubated at 22° C. for two days. The cultures are then transferred to MS-CIM medium with ticarcillin (400 mg/liter) to inhibit the growth of Agrobacterium. For constructs utilizing the PMI selectable marker gene (Reed et al., 2001), cultures are transferred to selection medium containing mannose as a carbohydrate source (MS with 2% mannose, 300 mg/liter ticarcillin) after 7 days, and cultured for 3-4 weeks in the dark. Resistant colonies are then transferred to regeneration induction medium (MS with no 2,4-D, 0.5 mg/liter IAA, 1 mg/liter zeatin, 200 mg/liter TIMENTIN®, 2% mannose, and 3% sorbitol) and grown in the dark for 14 days. Proliferating colonies are then transferred to another round of regeneration induction media and moved to the light growth room. Regenerated shoots are transferred to GA7 containers with GA7-1 medium (MS with no hormones and 2% sorbitol) for 2 weeks and then moved to the greenhouse when they are large enough and have adequate roots. Plants are transplanted to soil in the greenhouse (T₀ generation) grown to maturity and the T₁ seed is harvested.

IV.F.3. Transformation of Plastids

Seeds of Nicotiana tabacum c.v. ‘Xanthi nc’ are germinated seven per plate in a 1″ circular array on T agar medium and bombarded 12-14 days after sowing with 1 μm tungsten particles (M10, Bio-Rad Laboratories, Hercules, Calif., United States of America) coated with DNA from plasmids pPH143 and pPH145 essentially as disclosed (Svab & Maliga, 1993). Bombarded seedlings are incubated on T medium for two days after which leaves are excised and placed abaxial side up in bright light (350-500 mmol photons/m²/s) on plates of RMOP medium (Svab et al., 1990) containing 500 μg/ml spectinomycin dihydrochloride (Sigma, St. Louis, Mo., United States of America). Resistant shoots appearing underneath the bleached leaves three to eight weeks after bombardment are subcloned onto the same selective medium, allowed to form callus, and secondary shoots isolated and subcloned.

Complete segregation of transformed plastid genome copies (homoplasmicity) in independent subclones is assessed by standard techniques of Southern blotting (Sambrook & Russell, 2001). BamH I/EcoR 1-digested total cellular DNA (Mettler, 1987) is separated on 1% Tris-borate-EDTA (TBE) agarose gels, transferred to nylon membranes (Amersham Biosciences, Piscataway, N.J., United States of America) and probed with ³²P-labeled random primed DNA sequences corresponding to a 0.7 kb BamH IlHind III DNA fragment from pC8 containing a portion of the rps7/12 plastid targeting sequence. Homoplasmic shoots are rooted aseptically on spectinomycin-containing MS/IBA medium (McBride et al., 1994) and transferred to the greenhouse.

V. Plants, Breeding, and Seed Production

V.A. Plants

The presently disclosed subject matter also provides plants comprising the disclosed compositions. In some embodiments, the modification includes being enriched for an essential amino acid as a proportion of a polypeptide fraction of the plant. In some embodiments, the polypeptide fraction can be, for example, total seed polypeptide, soluble polypeptide, insoluble polypeptide, water-extractable polypeptide, and lipid-associated polypeptide. In some embodiments, the modification includes overexpression, underexpression, antisense modulation, sense suppression, inducible expression, inducible repression, or inducible modulation of a gene.

V.B. Breeding

The plants obtained via transformation with a nucleotide sequence of the presently disclosed subject matter can be any of a wide variety of plant species, including monocots and dicots; however, the plants used in the method for the presently disclosed subject matter are selected in some embodiments from the list of agronomically important target crops set forth hereinabove. The expression of a gene of the presently disclosed subject matter in combination with other characteristics important for production and quality can be incorporated into plant lines through breeding. Breeding approaches and techniques are known in the art. See e.g., Welsh, 1981; Wood, 1983; Mayo, 1987; Singh, 1986; Wricke & Weber, 1986.

The genetic properties engineered into the transgenic seeds and plants disclosed above are passed on by sexual reproduction or vegetative growth and can thus be maintained and propagated in progeny plants. Generally, the maintenance and propagation make use of known agricultural methods developed to fit specific purposes such as tilling, sowing, or harvesting. Specialized processes such as hydroponics or greenhouse technologies can also be applied. As the growing crop is vulnerable to attack and damage caused by insects or infections as well as to competition by weed plants, measures are undertaken to control weeds, plant diseases, insects, nematodes, and other adverse conditions to improve yield. These include mechanical measures such as tillage of the soil or removal of weeds and infected plants, as well as the application of agrochemicals such as herbicides, fungicides, gametocides, nematicides, growth regulants, ripening agents, and insecticides.

Depending on the desired properties, different breeding measures are taken. The relevant techniques are well known in the art and include, but are not limited to, hybridization, inbreeding, backcross breeding, multiline breeding, variety blend, interspecific hybridization, aneuploid techniques, etc. Hybridization techniques can also include the sterilization of plants to yield male or female sterile plants by mechanical, chemical, or biochemical means. Cross-pollination of a male sterile plant with pollen of a different line assures that the genome of the male sterile but female fertile plant will uniformly obtain properties of both parental lines. Thus, the transgenic seeds and plants according to the presently disclosed subject matter can be used for the breeding of improved plant lines that, for example, increase the effectiveness of conventional methods such as herbicide or pesticide treatment or allow one to dispense with said methods due to their modified genetic properties. Alternatively new crops with improved stress tolerance can be obtained, which, due to their optimized genetic “equipment”, yield harvested product of better quality than products that were not able to tolerate comparable adverse developmental conditions (for example, drought).

V.C. Seed Production

Some embodiments of the presently disclosed subject matter also provide seed and isolated product from plants that comprise an expression cassette comprising a promoter sequence operably linked to an isolated nucleic acid, the nucleotide sequence being selected from the group consisting of:

-   -   (a) a nucleotide sequence that hybridizes under highly stringent         conditions of hybridization of 65° C. in 6×SSC, followed by a         final washing step of at least 15 minutes at 65° C. in 0.1×SSC         to a nucleotide sequence as set forth in SEQ ID NO: 1, or         fragment, domain, or feature thereof;     -   (b) a nucleotide sequence encoding a polypeptide that is an         ortholog of a polypeptide of SEQ ID NO: 2, or a fragment, domain         or feature thereof;     -   (c) a nucleotide sequence complementary (for example, fully         complementary) to (a) or (b); and     -   (d) a nucleotide sequence that is the reverse complement (for         example, its full reverse complement) of (a) or (b) according to         the present disclosure.

In some embodiments the isolated product comprises an enzyme, a nutritional polypeptide, a structural polypeptide, an amino acid, a lipid, a fatty acid, a polysaccharide, a sugar, an alcohol, an alkaloid, a carotenoid, a propanoid, a steroid, a pigment, a vitamin, or a plant hormone.

Embodiments of the presently disclosed subject matter also relate to isolated products produced by expression of an isolated nucleic acid containing a nucleotide sequence selected from the group consisting of:

-   -   (a) a nucleotide sequence that hybridizes under highly stringent         conditions of hybridization of 65° C. in 6×SSC, followed by a         final washing step of at least 15 minutes at 65° C. in 0.1×SSC         to a nucleotide sequence as set forth in SEQ ID NO: 1, or a         fragment, domain, or feature thereof;     -   (b) a nucleotide sequence encoding a polypeptide that is an         ortholog of a polypeptide listed in SEQ ID NO: 2, or a fragment,         domain, or feature thereof;     -   (c) a nucleotide sequence complementary (for example, fully         complementary) to (a) or (b); and     -   (d) a nucleotide sequence that is the reverse complement (for         example, its full reverse complement) of (a) or (b) according to         the present disclosure.

In some embodiments, the product is produced in a plant. In some embodiments, the product is produced in cell culture. In some embodiments, the product is produced in a cell-free system. In some embodiments, the product comprises an enzyme, a nutritional polypeptide, a structural polypeptide, an amino acid, a lipid, a fatty acid, a polysaccharide, a sugar, an alcohol, an alkaloid, a carotenoid, a propanoid, a steroid, a pigment, a vitamin, or a plant hormone. In some embodiments, the product is a polypeptide comprising an amino acid sequence listed in SEQ ID NO: 2, or ortholog thereof. In some embodiments, the polypeptide comprises an enzyme.

In seed production, germination quality, and uniformity of seeds are essential product characteristics. As it is difficult to keep a crop free from other crop and weed seeds, to control seedborne diseases, and to produce seed with good germination, fairly extensive and well-defined seed production practices have been developed by seed producers who are experienced in the art of growing, conditioning, and marketing of pure seed. Thus, it is common practice for the farmer to buy certified seed meeting specific quality standards instead of using seed harvested from his own crop. Propagation material to be used as seeds is customarily treated with a protectant coating comprising herbicides, insecticides, fungicides, bactericides, nematicides, molluscicides, or mixtures thereof. Customarily used protectant coatings comprise compounds such as captan, carboxin, thiram (tetramethylthiuram disulfide; TMTD®; available from R. T. Vanderbilt Company, Inc., Norwalk, Conn., United States of America), methalaxyl (APRON XL®; available from Syngenta Corp., Wilmington, Del., United States of America), and pirimiphos-methyl (ACTELLIC®; available from Agriliance, LLC, St. Paul, Minn., United States of America). If desired, these compounds are formulated together with further carriers, surfactants, and/or application-promoting adjuvants customarily employed in the art of formulation to provide protection against damage caused by bacterial, fungal, or animal pests. The protectant coatings can be applied by impregnating propagation material with a liquid formulation or by coating with a combined wet or dry formulation. Other methods of application are also possible such as treatment directed at the buds or the fruit.

VI. Additional Applications

The presently disclosed subject matter also provides methods for targeting a protein of interest to a structure of a plant cell. In some embodiments, the structure is selected from the group including but not limited to endoplasmic reticulum (ER) and apoplast. In some embodiments, the method comprises (a) fusing a nucleic acid molecule encoding a signal sequence of a Zea mays Q protein in frame to a nucleotide sequence encoding the protein of interest, wherein the nucleic acid molecule encoding a signal sequence of a Zea mays Q protein and the nucleotide sequence encoding the protein of interest are operably linked to a promoter to produce a plant expression construct; and (b) transforming the plant cell with the plant expression construct, whereby the protein of interest is targeted to the structure. In some embodiments, the signal sequence corresponds to the first 19 amino acid of SEQ ID NO: 2.

As used herein, the term “protein of interest” refers to any polypeptide or polypeptide fragment for which the expression in a plant or plant cell would be desirable. Exemplary proteins of interest include, but are not limited to carbohydrases, cellulases, hemicellulases, pectinases, isomerases, lyases, proteases, heat shock proteins, chaperonins, phytases, insecticidal proteins, antimicrobial proteins, α-amylases, glucoamylases, glucanases, glucosidases, xylanases, ferulic acid esterases, galactosidases, pectinases, and chymosins. In some embodiments, the protein of interest is naturally occurring in the plant cell, but one or more extra copies of a nucleic acid sequence encoding the polypeptide of interest is provided as a transgene. In some embodiments, the protein of interest is heterologous to the plant or plant cell.

The presently disclosed subject matter also provides methods for producing a plant seed with an increased nutritional value. In some embodiments, the method comprises (a) transforming a plant cell with an expression vector comprising a nucleotide sequence encoding SEQ ID NO: 2, or a fragment or derivative thereof; (b) regenerating a plant from the transformed plant cell; and (c) isolating a seed from the regenerated plant, whereby a seed with an increased nutritional value is produced.

As used herein, the phrase “a seed with increased nutritional value” refers to a seed that has been modified such to contain a polypeptide that is not normally found in the seed or contains an elevated amount of a polypeptide that is normally found in the seed. In some embodiments, the polypeptide that is not normally found in the seed is a derivative of a protein that the seed normally contains. Such a derivative can be characterized, for example, by a modification of the amino acid sequence of a naturally occurring protein to include a higher content of one or more amino acids (for example, an increased proportion of one or more essential amino acids), an improved amino acid balance, and/or an improved amino acid digestibility when compared to a seed from a non-transformed plant of the same species. These modifications of the amino acid sequence can be accomplished by mutagenesis of a nucleotide sequence encoding the polypeptide using techniques that are known to the skilled artisan.

The presently disclosed subject matter also provides methods for targeting a protein of interest to a protein body in a plant. In some embodiments, the method comprises (a) fusing a nucleic acid molecule encoding SEQ ID NO: 2, or a fragment or derivative thereof, in frame to a nucleotide sequence encoding the protein of interest, wherein the nucleic acid molecule encoding SEQ ID NO: 2, or the fragment or derivative thereof, and the nucleotide sequence encoding the protein of interest are operably linked to a promoter to produce a plant expression construct; and (b) transforming the plant cell with the plant expression construct, whereby the protein of interest is targeted to a protein body in the plant. In some embodiments, the nucleic acid molecule encoding SEQ ID NO: 2, or a fragment or derivative thereof, which is fused in frame to a nucleotide sequence encoding the protein of interest includes a nucleotide sequence encoding a protease cleavage site between the nucleic acid molecule encoding SEQ ID NO: 2, or a fragment or derivative thereof, and the nucleotide sequence encoding the protein of interest.

Proteases for which a cleavage site can be introduced in the fusion protein, and the amino acid sequences of recognized cleavage sites, are known in the arts of molecular biology and protein expression, and include, but are not limited to Factor Xa, thrombin, the family of caspases, chymotrypsin, pepsin, tobacco etch virus protease, and trypsin. See Sambrook & Russell, 2001, and references cited therein, for a discussion of the use of proteases to cleave fusion proteins. The protease can be chosen based upon its recognition sequence, for example, based on the absence of the recognition sequence in the protein of interest, such that when the fusion protein is treated with the protease, the protein of interest will be released from the Q protein (or fragment or derivative thereof) intact. Additional purification steps that are known to the skilled artisan can then be used to purify the protein of interest. These techniques include affinity purification (if an antibody to the protein of interest is available), SDS-PAGE separation, size based chromatography, or any other method available to the skilled artisan.

EXAMPLES

The following Examples have been included to illustrate representative and exemplary modes of the presently disclosed subject matter. In light of the present disclosure and the general level of skill in the art, those of skill will appreciate that the following Examples are intended to be exemplary only and that numerous changes, modifications, and alterations can be employed without departing from the spirit and scope of the presently disclosed subject matter.

Standard recombinant DNA and molecular cloning techniques used here are well known in the art and are disclosed in Sambrook & Russell, 2001; Silhavy et al., 1984; Ausubel et al., 2002; Ausubel et al., 2003; Reiter et al., 1992; and Schultz et al., 1998.

Example 1 Isolation of Promoter/Genomic Clones Corresponding to the Q Protein Gene

The nucleotide sequence from the Q protein ORF (SEQ ID NO: 1) was used to design primers for genomic walking. A genomic clone corresponding to the Q protein cDNA was isolated via PCR utilizing maize libraries based on the GENOME WALKER™ kit (BD Biosciences Clontech, Palo Alto, Calif., United States of America) as template. GENOME WALKER™ adaptor-ligated maize genomic libraries were constructed using DNA from maize cultivar 6N615. Five different libraries were constructed, each comprising genomic DNA fragments generated by digestion with one of the following blunt end restriction enzymes: Dra I, EcoR V, Hinc II, Ssp I, or Stu I. GENOME WALKER™ libraries were screened utilizing one or more of the gene specific primers QP1 (SEQ ID NO: 4) and QP2 (SEQ ID NO: 5) with the adaptor primer supplied in the kit. PCR conditions were those suggested in BD Bioscience Clontech's user's manual. PCR products were fractionated on agarose gels, and the resulting product band was excised, subcloned into a TOPO® vector (Invitrogen Corp., Carlsbad, Calif., United States of America) and sequenced to verify the correct product. A 516 base pair genomic clone corresponding to the Q protein gene was cloned from the Dra I GENOME WALKER™ library.

Example 2 Activity of the Q Promoter

Transgenic maize plants were stably transformed with binary vector 11037 using Agrobacterium-mediated transformation. Vector 11037 is identical to pNOV4061 (SEQ ID NO: 14: see also PCT International Patent Application Publication WO 03/57248) with the exception that the γ-zein promoter found in the phytase expression cassette in pNOV4061 is replaced with the Q promoter (SEQ ID NO: 6) in vector 11037. The gene product of the phytase expression cassette in vector 11037 is presented in SEQ ID NO: 12, and is identical to SEQ ID NO: 6 of PCT International Patent Application Publication WO 03/57248. It includes the 19 amino acid signal sequence from the 27 kDa γ-zein (corresponds to the first 19 amino acids of SEQ ID NO: 12), Nov9x phytase, and the hexapeptide SEKDEL (SEQ ID NO: 11).

T1 seed were harvested from plants regenerated from maize tissue transformed with vector 11037. Seed were pulverized and soluble proteins were extracted from flour samples using extraction buffer (50 mM Tris-HCl, pH 8.0, 100 mM NaCl, 2 mM EDTA). Flour suspensions were incubated at room temperature for 60 minutes with agitation, and insoluble material was removed by centrifugation.

The measurement of phytase activity and detection of Nov9x phytase by Western blot analysis was performed as described in Example 3 of PCT WO 03/57248. All reagents and reaction conditions were as described in WO 03/57248, and all reagent volumes were adjusted proportionately. Briefly, the measurement of phytase activity is based on the detection of inorganic phosphate released from sodium phytate substrate by the hydrolytic action of phytase. Phytase assay procedures were adapted from the protocols of Wyss et al., 1999 and Engelen et al., 2001.

Phytase activity in flour samples from single kernels and pooled kernels was measured at pH 5.5 and 37° C. Assay results for eight samples of T1 seed harvested from two regenerated transgenic plants (plants A and B) are presented in Table 1. Sample 305B-11A represents the phytase activity extracted from a control corn flour sample containing Nov9x phytase. The samples were listed in order of decreasing phytase activity. TABLE 1 Demonstration of Phytase Activity in Transgenic Corn Flour Phytase Units per Sample^(a) Gram of Corn Flour 305B-11A (positive control) 1775 Plant A, seed #3 451 Plant A, seed 10 392 Plant B, seed 5 314 Plant A, seed 4 292 Plant B (pooled seed) 291 Plant B, seed 4 255 Plant B, seed 7 204 Plant A, seed 5 191 ^(a)Each sample was from a numbered, single seed, with the exception of the sample designated as a pooled seed, which corresponds to 10 T1 kernels pulverized together.

Flour extracts analyzed in Table 1 were also analyzed by Western blot analysis using antisera to purified Nov9x phytase as shown in FIG. 1. The first lane on the blot depicted in FIG. 1 indicates the positions of molecular weight standards (labeled on left). A188 is an extract of seed from non-transgenic corn. Nov9x phytase is identified as the prominent band migrating in the region of the 55 kDa standard. Nov9x phytase was not detected in the A188 corn flour extract.

Example 3 SDS-PAGE Analysis of Proteins Extracted from Seeds

Dried kernels from Hi-II x A188 maize were soaked in distilled water at 4° C. overnight. Endosperm and embryos were separated and frozen at −80° C. Frozen tissue was pulverized using a KLECO tissue pulverizer (KLECO, Visalia, Calif., United States of America). Proteins were extracted from endosperm flour by addition of 500 μl extraction buffer (50 mM HEPES, pH 8, 2 mM EDTA, 100 mM NaCl, and 4 mM DTT) for every 100 mg flour. Samples were vortexed and rocked at room temperature for 40 minutes. Proteins were extracted from the embryo paste by addition of 2.5 ml extraction buffer for every 100 mg tissue. A portion of the soluble fraction was heated at 80° C. for 20 minutes, and aggregated proteins were removed by centrifugation. Samples of the extract before (−) and after (+) heating were analyzed by SDS-PAGE (see FIG. 2).

Discussion of Examples 1-3

A 55 kDa Protein is the second most abundant Protein released from endosperm flour in buffer and DTT. In the course of testing different conditions for extracting a recombinant thermostable enzyme from maize flour, an abundant endosperm protein of 55 kDa was identified that remained soluble during heating at 80° C. (Example 3, FIG. 2). The 55 kDa protein was the second most abundant protein released from endosperm flour in buffer containing 100 mM NaCl and 4 mM DTT. The most abundant protein in these extracts was the 27 kDa γ-zein, a maize prolamin that typically constitutes 15% of total endosperm protein.

A similar endosperm fraction was described by Vitale et al., 1982. They incubated protein bodies in the presence of DTT or β-ME and characterized proteins in the soluble fraction. The two most abundant proteins released from protein bodies under these conditions had molecular weights of 28,000 and 58,000. Proteins in this fraction were named “Reduced Soluble Proteins” or RSPs.

An EST in GENBANK® matches the first 20 codons of the 55 kDa protein and encodes a Polypeptide chain of 171 residues. The amino acid sequences at the amino-termini of the 27 kDa and 55 kDa proteins discussed above were determined. The partial sequence of the 27 kDa protein was THTSGGXXXQPPPPVHLLPP (SEQ ID NO: 7). This sequence matches the amino-terminus of the 28 kDa maize glutelin-2 (γ-zein; Prat et al., 1985; Boronat et al., 1986).

The partial sequence of the 55 kDa protein was TQTGGCSCGQQQSHEQQHHP (SEQ ID NO: 8). A search of the PIR and SwissProt databases did not identify any matches to this sequence. However, when a back-translated DNA sequence was used to screen GENBANK®, the query sequence matched at each codon with an expressed sequence tag (EST) from an endosperm cDNA library (GENBANK® Accession No. A1812147). Translation of the EST sequence starting with the codon that corresponds to the amino-terminus of the 55 kDa protein yields a deduced polypeptide chain of 171 residues.

Cloning of two overlapping cDNAs that encode a protein of 289 residues (molecular weight 34,000). Oligonucleotide primers against the EST sequence were used to amplify a cDNA clone from a maize cDNA library. The predicted stop codon in the EST sequence was found to encode a Leu in the new clone, and the ORF continued to the end of the cloned sequence. A second cDNA clone that overlapped with the 3′ end of the first was amplified from the same library. The new ORF encoded an additional 118 amino acids, for a total of 289. The calculated molecular weight of the deduced protein is 34,000. The discrepancy between the calculated molecular weight (34,000) and that estimated from SDS-PAGE analysis (55,000) could be due to unusual structural features related to the abundance of Gln residues. The amino acid composition of the deduced protein is shown in Table 2. TABLE 2 Amino Acid Composition of Zeins Amino zein- zein- zein- zein- zein- zein- SEQ ID Acid α19 α22 β15 δ10 δ18 γ27 NO: 2 A 29 34 23 7 9 10 6 C 2 1 7 5 3 15 16 D 0 0 1 1 0 0 3 E 1 2 3 0 0 2 13 F 13 8 0 5 5 2 3 G 5 2 14 4 5 13 11 H 2 3 0 3 3 16 29 I 9 11 1 3 8 4 8 K 0 0 0 0 1 0 5 L 43 42 16 15 13 19 11 M 0 5 18 29 53 1 4 N 10 13 3 3 3 0 8 P 23 22 14 20 35 51 16 Q 41 51 26 15 15 30 104 R 2 4 5 0 0 5 4 S 15 17 8 8 18 8 23 T 5 7 5 5 10 9 6 V 5 17 3 5 5 15 9 W 0 0 0 0 2 0 0 Y 8 7 14 1 2 4 10 Total 213 246 161 129 190 204 289

The amino acid sequence at the C-terminus shows homology to prolamins, the seed storage proteins of cereals. The amino acid sequence from residues 172-289 of the mature protein shows homology to prolamins of several cereals including maize, rice, and barley. Sequence identities range from 36-53% for stretches of 58-118 residues: 37% (44/116 residues) for a rice prolamin, 38% (46/118) for a maize zein, 36% (40/115) for the sorghum prolamin γ-kafirin, 53% (31/58) for oat avenin, and 55% (33/59) for barley B-hordein. Identity with 27 kDa γ-zein (glutelin-2) was 38% over a stretch of 119 residues (46 matches). The homologous region was limited to the C-terminal domain of γ-zein.

The amino acid compositions of the major zeins are included in Table 2 for comparison with the 55 kDa protein. The deduced sequence is remarkable by comparison to the other zeins with respect to relative levels of three amino acids: the deduced sequence contains 106 Gln, 13 Glu, and 5 Lys out of 289 total residues. All other zeins have 0 Lys, except for the 18 kDa 6-zein, which has just 1.

The percent composition of each amino acid in the deduced protein and other zeins is shown in Table 3. The 55 kDa protein contains 36% Gln. By comparison, the α-zeins are the next most Gln-rich prolamins and contain only 20% Gln. The 55 kDa protein also has the lowest Pro content of maize prolamins. The amino acid composition of the 58 kDa RSP characterized by Vitale et al., 1982 is displayed side-by-side with that for the 55 kDa protein. TABLE 3 Percent Composition of Amino Acids in Zeins SEQ Amino zein- zein- zein- zein- zein- zein- ID 58 kD Acid α19 α22 β15 δ10 δ18 γ27 NO: 2 RSP G 2.3 0.8 8.7 3.1 2.6 6.4 3.8 4.9 A 13.6 13.8 14.3 5.4 4.7 4.9 2.1 3.5 V 2.3 6.9 1.9 3.9 2.6 7.4 3.1 5.1 L 20.2 17.1 9.9 11.6 6.8 9.3 3.8 4.7 I 4.2 4.5 0.6 2.3 4.2 2.0 2.8 2.2 M 0.0 2.0 11.2 22.5 17.9 0.5 1.4 1.3 F 6.1 3.3 0.0 3.9 2.6 1.0 1.0 1.9 W 0.0 0.0 0.0 0.0 1.1 0.0 0.0 0.0 K 0.0 0.0 0.0 0.0 0.5 0.0 1.7 2.6 P 10.8 8.9 8.7 15.5 18.4 25.0 5.5 4.7 C 0.9 0.4 4.3 3.9 1.6 7.4 5.5 4.4 S 7.0 6.9 5.0 6.2 9.5 3.9 8.0 7.3 T 2.3 2.8 3.1 3.9 5.3 4.4 2.1 2.5 Y 3.8 2.8 8.7 0.8 1.1 2.0 3.5 3.5 N 4.7 5.3 1.9 2.3 1.6 0.0 2.8 4.3 D 0.0 0.0 0.6 0.8 0.0 0.0 1.0 Q 19.2 20.7 16.1 11.6 7.9 14.7 36.0 33.6 E 0.5 0.8 1.9 0.0 0.0 1.0 4.5 H 0.9 1.2 0.0 2.3 1.6 7.8 10.0 11.0 R 0.9 1.6 3.1 0.0 0.0 2.5 1.4 2.1 SUM 100.0 100.0 100.0 100.0 100.0 100.0 100.0 99.6

Example 4 Accumulation of a Q Protein Fusion Protein in Transgenic Seed

Construct 11045 was a binary vector encoding a fusion protein of the full-length Q protein linked to an α-galactosidase enzyme from T. maritima with a tripeptide linker Gly-Gly-Ala. The gene encoding the fusion protein was operably linked to the promoter of the 27 kDa gamma-zein protein (SEQ ID NO: 13). Primers were designed to isolate a nucleotide sequence encoding the Q-protein from pNOV4349 (SEQ ID NO: 17, of which nucleotides 10061-10090 correspond to the Q-protein coding sequence) while adding a 9 bp sequence encoding the tripeptide linker to the 3′ end. 3′ Nco 1 and 5′ BamH I sites were added to the ends of the PCR product. The 953 bp PCR fragment was amplified from pNOV4349 and cut with BamH I and Nco 1, then inserted into the 5227 bp BamH I/Nco I fragment from pNOV4325 (SEQ ID NO: 16; nucleotides 3565-5901 encode the α-galactosidase polypeptide). This plasmid was named pWIN010. Construct pWIN010 was then cut with Kpn I and Hind III, and the 3489 bp fragment was ligated to the 9154 bp Kpn I/Hind III fragment from binary vector pNOV2117 (SEQ ID NO: 15; see also PCT International Patent Application Publication WO 03/57248).

Transgenic maize plants were stably transformed with binary vector 11045 using Agrobacterium-mediated transformation. T1 seed were harvested from plants regenerated from maize tissue transformed with vector 11045. Seeds were pulverized and soluble proteins were extracted from flour samples using extraction buffer (50 mM Tris-HCl, pH 8.0, 100 mM NaCl, 2 mM EDTA). Flour suspensions were incubated at room temperature for 60 minutes with agitation, and insoluble material was removed by centrifugation. The corn flour samples were then analyzed for α-galactosidase activity. α-galactosidase activity results are presented in Table 4. TABLE 4 α-galactosidase Activity in Trangenic Maize α-galactosidase Sample ID Construct units per g of flour MD9L011883 11045 4.06 MD9L011893 11045 9.31 MD9L01I901 11045 8.39 MD9L011903 11045 9.28 MD9L011912 11045 7.79 Negative Corn Flour (none) −0.78

The measurement of α-galactosidase activity was based on the colorimetric assay involving the release of p-nitrophenol from p-nitrophenyl α-d-galactopyranoside as described in Liebl et al., 1998.

As shown in Table 4, the α-galactosidase activity of transgenic maize containing construct 11045 encoding the Q-protein/α-galactosidase fusion protein showed an increase in α-galactosidase activity above the negative corn flour control. The levels ranged from 4 α-galactosidase units/gram offlourto 9 α-galactosidase units/gram of flour. The negative corn flour control has no α-galactosidase activity. These results are also presented in FIG. 3.

Example 5 The Q Protein Signal Sequence Directs Accumulation of a Fusion Protein to Transgenic Seed

Binary vector 12173 was made by designing primers to isolate the Q protein signal sequence (amino acids 1-19 of SEQ ID NO: 2) from pNOV4349 while adding a 3′ Nco I and a 5′ BamH I site to the ends of the PCR product. The 80 bp PCR fragment was amplified from pNOV4349 and cut with BamH I and Nco I, then inserted into the 5226 bp BamH I/Nco I fragment from pNOV4328 (SEQ ID NO: 18; nucleotides 3621-5279 encode the α-galactosidase polypeptide). This plasmid was named pWIN013New. pWIN013New was then cut with Kpn I and Hind III, and the 2614 bp fragment was ligated to the 9154 bp Kpn I/Hind III fragment from binary vector pNOV2117 (SEQ ID NO: 15; see also PCT International Patent Application Publication WO 03/57248). This construct was named binary vector 12173. It encodes a fusion protein containing the 19 amino acid signal sequence from the Q protein (corresponds to the first 19 amino acid of SEQ ID NO: 2) fused to the α-galactosidase protein under the transcriptional control of a maize 27 kDa gamma zein promoter (SEQ ID NO: 13).

Transgenic maize plants were stably transformed with binary vector 12173 using Agrobacterium-mediated transformation. T1 seed were harvested from plants regenerated from maize tissue transformed with binary vector 12173. Seed were pulverized and soluble proteins were extracted from flour samples using extraction buffer (50 mM Tris-HCl, pH 8.0, 100 mM NaCl, 2 mM EDTA). Flour suspensions were incubated at room temperature for 60 minutes with agitation, and insoluble material was removed by centrifugation. The corn flour samples were then analyzed for α-galactosidase activity. α-galactosidase activity results are presented in Table 5. TABLE 5 α-galactosidase Activity in Trangenic Maize α-galactosidase units Sample ID Construct per g flour MD9L020749 12173 70.848 MD9L020735 12173 68.175 MD9L030752 12173 52.274 MD9L020758 12173 43.160 MD9L019976 12173 23.976 MD9L019782 12173 11.877 MD9L019766 12173 2.566 Negative Corn Flour N/A −0.782

The α-galactosidase activity resulting from the presence of construct 12173 containing the Q protein signal sequence showed the increased presence of the α-galactosidase protein. The levels ranged from 3 α-galactosidase units/gram of flour to 71 α-galactosidase units/gram of flour. The negative corn flour control had no α-galactosidase protein. These results are also presented in FIG. 4.

REFERENCES

The references listed below, as well as all references cited in the specification, are incorporated herein by reference in their entireties to the extent that they supplement, explain, provide a background for, or teach methodology, techniques, and/or compositions employed herein.

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It will be understood that various details of the presently disclosed subject matter can be changed without departing from the scope of the presently disclosed subject matter. Furthermore, the foregoing description is for the purpose of illustration only, and not for the purpose of limitation. 

1. A method for expressing a nucleotide sequence in a plant, the method comprising: (a) operably linking the nucleotide sequence to a promoter comprising SEQ ID NO: 6 to produce an expression cassette; and (b) generating a transgenic plant comprising the expression cassette, whereby the nucleotide sequence is expressed in the plant.
 2. The method of claim 1, wherein the generating comprises transforming a plant cell with the expression cassette and regenerating the plant from the transformed plant cell.
 3. The method of claim 2, wherein the transforming is by biolistic transformation of a vector comprising the expression cassette.
 4. The method of claim 3, wherein the vector is a binary Agrobacterium expression vector.
 5. The method of claim 1, wherein the generating comprises homologously recombining the nucleotide sequence into an endogenous genetic locus under the control of a promoter comprising SEQ ID NO:
 6. 6. The method of claim 1, wherein the nucleotide sequence encodes a polypeptide selected from the group consisting of carbohydrases, cellulases, hemicellulases, pectinases, isomerases, lyases, proteases, heat shock proteins, chaperonins, phytases, insecticidal proteins, antimicrobial proteins, α-amylases, glucoamylases, glucanases, glucosidases, xylanases, ferulic acid esterases, galactosidases, pectinases, and chymosin.
 7. The method of claim 1, wherein the plant is selected from the group consisting of rice, maize, wheat, barley, oats, rye, millet, sorghum, triticale, secale, einkorn, spelt, emmer, teff, milo, flax, gramma grass, Tripsacum, and teosinte.
 8. An isolated nucleic acid molecule comprising SEQ ID NO:
 6. 9. An expression cassette comprising SEQ ID NO:
 6. 10. A recombinant vector comprising the expression cassette of claim
 9. 11. A cell comprising the expression cassette of claim
 9. 12. A transgenic plant comprising the expression cassette of claim
 9. 13. The transgenic plant of claim 12, wherein the plant is a monocot.
 14. The transgenic plant of claim 13, wherein the monocot is selected from the group consisting of rice, maize, wheat, barley, oats, rye, millet, sorghum, triticale, secale, einkorn, spelt, emmer, teff, milo, flax, gramma grass, Tripsacum, and teosinte.
 15. The transgenic plant of claim 13, wherein the plant is selected from the group consisting of rice, wheat, barley, rye, maize, potato, canola, soybean, sunflower, carrot, sweet potato, sugarbeet, bean, pea, chicory, lettuce, cabbage, cauliflower, broccoli, turnip, radish, spinach, asparagus, onion, garlic, eggplant, pepper, celery, squash, pumpkin, cucumber, apple, pear, quince, melon, plum, cherry, peach, nectarine, apricot, strawberry, grape, raspberry, blackberry, pineapple, avocado, papaya, mango, banana, soybean, tobacco, tomato, sorghum and sugarcane.
 16. The transgenic plant of claim 15, wherein the plant is maize.
 17. The transgenic plant of claim 13, wherein the expression cassette is expressed in a tissue selected from the group consisting of the epidermis, root, vascular tissue, meristem, cambium, cortex, pith, leaf, flower, seed, and combinations thereof.
 18. The transgenic plant of claim 17, wherein the expression cassette is expressed in a seed and a polypeptide encoded by the nucleotide sequence is located within a protein body of endoplasmic reticulum of a cell of the seed.
 19. A method for expressing a nucleotide sequence in a plant, the method comprising: (a) operably linking the nucleotide sequence to a plant promoter, the nucleotide sequence comprising SEQ ID NO: 1 to produce an expression cassette; and (b) generating a transgenic plant comprising the expression cassette, whereby the nucleotide sequence is expressed in the plant.
 20. The method of claim 19, wherein the generating comprises transforming a plant cell with the expression cassette and regenerating the plant from the transformed plant cell.
 21. The method of claim 20, wherein the transforming is by biolistic transformation of a vector comprising the expression cassette.
 22. The method of claim 21, wherein the vector is a binary Agrobacterium expression vector.
 23. The method of claim 19, wherein the plant is selected from the group consisting of rice, maize, wheat, barley, oats, rye, millet, sorghum, triticale, secale, einkorn, spelt, emmer, teff, milo, flax, gramma grass, Tripsacum, and teosinte.
 24. An isolated nucleic acid molecule comprising SEQ ID NO:
 1. 25. An expression cassette comprising SEQ ID NO:
 1. 26. A recombinant vector comprising the expression cassette of claim
 25. 27. A cell comprising the expression cassette of claim
 25. 28. A transgenic plant comprising the expression cassette of claim
 25. 29. The transgenic plant of claim 28, wherein the plant is a monocot.
 30. The transgenic plant of claim 29, wherein the monocot is selected from the group consisting of rice, maize, wheat, barley, oats, rye, millet, sorghum, triticale, secale, einkorn, spelt, emmer, teff, milo, flax, gramma grass, Tripsacum, and teosinte.
 31. The transgenic plant of claim 29, wherein the plant is selected from the group consisting of rice, wheat, barley, rye, maize, potato, canola, soybean, sunflower, carrot, sweet potato, sugarbeet, bean, pea, chicory, lettuce, cabbage, cauliflower, broccoli, turnip, radish, spinach, asparagus, onion, garlic, eggplant, pepper, celery, squash, pumpkin, cucumber, apple, pear, quince, melon, plum, cherry, peach, nectarine, apricot, strawberry, grape, raspberry, blackberry, pineapple, avocado, papaya, mango, banana, soybean, tobacco, tomato, sorghum and sugarcane.
 32. The transgenic plant of claim 31, wherein the plant is maize.
 33. The transgenic plant of claim 29, wherein the expression cassette is expressed in a tissue selected from the group consisting of the epidermis, root, vascular tissue, meristem, cambium, cortex, pith, leaf, flower, seed, and combinations thereof.
 34. The transgenic plant of claim 33, wherein the expression cassette is expressed in seed and a polypeptide comprising SEQ ID NO: 2 is located within a protein body of endoplasmic reticulum of a cell of the seed.
 35. A method of producing a heterologous polypeptide in a plant cell, the method comprising: (a) generating a plant cell comprising a nucleotide sequence encoding the heterologous polypeptide operably linked to SEQ ID NO: 6; and (b) expressing in the plant cell the nucleotide sequence encoding the heterologous polypeptide, whereby the heterologous polypeptide is produced in the plant cell.
 36. The method of claim 35, wherein the generating comprises transforming the plant cell with an expression cassette comprising the nucleotide sequence encoding the heterologous polypeptide.
 37. The method of claim 36, wherein the transforming is by biolistic transformation of a vector comprising the expression cassette.
 38. The method of claim 37, wherein the vector is a binary Agrobacterium expression vector.
 39. The method of claim 35, wherein the generating comprises homologously recombining the nucleotide sequence into an endogenous genetic locus under the control of a promoter comprising SEQ ID NO: 6 such that the nucleotide sequence becomes operably linked to SEQ ID NO:
 6. 40. The method of claim 35, wherein the nucleotide sequence encodes a polypeptide selected from the group consisting of carbohydrases, cellulases, hemicellulases, pectinases, isomerases, lyases, proteases, heat shock proteins, chaperonins, phytases, insecticidal proteins, antimicrobial proteins, α-amylases, glucoamylases, glucanases, glucosidases, xylanases, ferulic acid esterases, galactosidases, pectinases, and chymosin.
 41. The method of claim 35, wherein the plant is selected from the group consisting of rice, maize, wheat, barley, oats, rye, millet, sorghum, triticale, secale, einkorn, spelt, emmer, teff, milo, flax, gramma grass, Tripsacum, and teosinte.
 42. The method of claim 35, further comprising regenerating a plant from the plant cell.
 43. The method of claim 35, further comprising isolating the polypeptide from the plant.
 44. The method of claim 43, wherein the polypeptide is located within a protein body of endoplasmic reticulum of the plant cell.
 45. A method of targeting a protein of interest to a structure of a plant cell selected from the group consisting of endoplasmic reticulum (ER) and apoplast, the method comprising: (a) fusing a nucleic acid molecule encoding a signal sequence of a Zea mays Q protein in frame to a nucleotide sequence encoding the protein of interest, wherein the nucleic acid molecule encoding a signal sequence of a Zea mays Q protein and the nucleotide sequence encoding the protein of interest are operably linked to a promoter to produce a plant expression construct; and (b) transforming the plant cell with the plant expression construct, whereby the protein of interest is targeted to the structure.
 46. A method of producing a plant seed with an increased nutritional value, the method comprising: (a) transforming a plant cell with an expression vector comprising a nucleotide sequence encoding SEQ ID NO: 2, or a fragment or derivative thereof; (b) regenerating a plant from the transformed plant cell; and (c) isolating a seed from the regenerated plant, whereby a seed with an increased nutritional value is produced.
 47. The method of claim 46, wherein the increased nutritional value is selected from the group consisting of an increased level of an essential amino acid, an improved amino acid balance, and an improved amino acid digestibility, when compared to a seed from a non-transformed plant of the same species.
 48. A method of targeting a protein of interest to a protein body in a plant, the method comprising: (a) fusing a nucleic acid molecule encoding SEQ ID NO: 2, or a fragment or derivative thereof, in frame to a nucleotide sequence encoding the protein of interest, wherein the nucleic acid molecule encoding SEQ ID NO: 2, or the fragment or derivative thereof, and the nucleotide sequence encoding the protein of interest are operably linked to a promoter to produce a plant expression construct; and (b) transforming the plant cell with the plant expression construct, whereby the protein of interest is targeted to a protein body in the plant. 